Model of structure of Jomon pit houses (Tokoro Archaeological Center)
The typical Jomon house was pit house that had a main pillar, whose hole was dug the widest and deepest into the ground, that was surrounded by other wooden upright supporting posts.
Earlier houses tended to be conical or have floors that were circular.
Earlier pit houses were round.
This one has a smoking ditch beside the entrance. (Reconstructed pit house, Kushiro Marsh, Hokkaido) 
The roofs, supported by five or six posts and a central pillar, were thatched with kaya (miscanthus) grass that helped drain off rainwater into the surrounding ditches.
Later pit houses became square with rounded off corners (Reconstructed pit house, Kushiro Marsh, Hokkaido)
The earthen floors tamped hard, were sometimes sunk half a metre into the ground, or sometimes covered in flagstone.
Indoor fireplaces were common as were storage pits and smoking ditches.
Apart from the common pit dwelling houses, some settlements had raised buildings that were probably storage houses or warehouses. Hundreds of these raised storage houses and more than 800 pit houses were found at the site of the Sannai Maruyama village. In addition, the large building with huge columns is an outstanding architectural feature of the Sannai-Maruyama ruins. 
Raised warehouse beside a pit dwelling on the Omusaro Plateau near Monbetsu
Longhouses were built in the largest settlements of the Jomon era. At the Aizu-Wakamatsu site in Fukushima prefecture, longhouses were excavated from a ring-shaped settlement surrounded by drainage ditches that was of the Middle Jomon period between 4,000 to 5,000 years ago. Three fireplaces fit one longhouse.
Longhouse at Sannai Maruyama
It appears that the Jomon people were skilled in working with wood from an early period. The Jomon people cut down trees to size for building things and for erecting buildings. From the Sakuramachi site in Toyama prefecture of the Middle Jomon period, a large number of wooden items, including more than 100 wooden beams, crosspieces, and posts were found.
The oldest piece of wood used in Jomon construction is reported to have been found in the Yokoo site in Oita prefecture is dated to 10,000 years ago. The 3.8 meter-long piece of wood (had six circular joint holes in it about 3 centimeters in diameter and) is thought to be a roof beam from a house built on stilts.
Several other pieces of Jomon construction timber from the Oyabe site in Toyama prefecture dated to 4,500 years ago, revealed that the Jomon people were already using an advanced construction technique called watariago-shiguchi in Japanese. The technique that joined building timbers together with a mortise and tennon joint into the form of a wooden cross, was used in the 7th century structure of the Horyuji Temple which is oldest surviving wooden building in the world.
Woodworking was an important craft or skill for the Jomon people, used for making dugout canoes, wooden vessels and especially for building. The Jomon people made wooden frames for the walls of storage pits and for the posts of their buildings.
They had learnt to use and work with many kinds of trees including chestnut, Japanese cedar tree (Cryptomeria japonica), mukunoki (Aphananthe aspera), inugaya (Cephalotaxus harringtonia), Japanese nutmeg (Torreya nucifera or kaya), camphor (Cinamonium camphora or kusunoki).
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Sources and readings:
Ancient Jomon of Japan by Junko Habu
Heritage of Japan 
Is a key differential between Japanese and Korean Jomon cultures the presence or lack of a central main pillar? None of the recreated prehistoric homesteads in Korea that I have visited had a central pillar (e.g. Daepyeong).
I’m certainly enjoying perusing your pages! Well done!
(Maybe I should not use the term Korean Jomon culture. I mean a Korean culture contemporary with Japanese Jomon culture.)
I found you one reconstructed drawing of a Paleolithic dwelling based on archaeology of the Kostenski site scroll down to the middle of this page sunken floor of dwelling, fireplace in the middle may well have been the origin of the Palaeolithic as well as initial Jomon architecture. The tool kit is similar to that found in the north of Japan. Source: “les mammouths – Dossiers Archéologie – n° 291 – Mars 2004”
Thanks for that link.
I also found something interesting at:
http://www.aerobiologicalengineering.com/wxk116/StoneAge/Habitats/
Excellent material. The picture (near the bottom of the page of your reference) has Upper Paleolithic huts from Buret (or Buryatia), Siberia dating to about 10,000 BCE that are exactly like the Jomon skeletal structures for pit dwellings, a perfect match since the Jomon people are known to be haplogroup D2 carriers and related to the ancestors of the Buryat people.
Thank you for the info, I am always fascinated with the Jomon and Ainu, because they seem to have so much in common with Polynesians. In Samoa, we too have round houses, but that has gone out of fashion, some are still around, but also the fact we too had a central pillar and the fire was in the center. The posts around the house are very significant when it comes to chiefly ceremonies, even to this day, and I wonder if the Jomon had cultural meaning for their central pillar and posts like we do. We used to have storehouses like the Jomon, and particularly the New Zealand Maori who had to adapt to the cold, have almost identical style store houses where they kept food high off the ground. Like the Jomon, we too have many sacred and taboo things in every day life, and our myths and legends are animist and of nature (of course today, most of us are Christian, but cultural traditions are still strong). Apparently, each family had a specific animal that they worshipped, anything from whales to bats. Maybe I’m reading too much into it, but the people of the Pacific seem more culturally tied than the scientists like to admit.
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