Formed by group of islands, the natural physical structure that Japan plays a big role in its vernacular architecture. Because natural environment is an important matter that shapes architecture, wants to be in harmony with structures and integrates with human needs. The characteristics of the nature play a major role in shaping the developing civilizations there. In this context, the fact that Japan has monsoon climate is geologically located on the earthquake zone and has a sloping topography, which are the most striking features in the formation of architecture. Built with local natural wood, reed and bamboo-like materials Traditional Japanese house are structures with raised floor, on raised legs, has a design concept that integrates with nature, not defying nature with its physical environment. In the formation of the skeletal system minding that structures have a limited lifetime, instead of nails, dove-tail joints are preferred that conduces flexible designs. In the traditional Japanese house where the minimal sense of space is embraced, the construction techniques and interior designs are more carefully considered due to the earthquakes. Thus, the structure and the physical surroundings are confronted as parts of an organic whole complementing to each other. The purpose of this study is to show how natural environmental data plays an important role in shaping the traditional Japanese house. Instead of resting with nature, listening to it and being in communication shows that there will be more positive and lively outcomes for the users.