This Study is concerned with the Style of Korean and Japanese wooden church architecture. The main subject of the study is to investigate the commonness and difference between Korean and Japanese wooden church architecture in the early period. In carrying this study into execution, I examined the architectural and historical backgrounds, and analysed the space, design elements, techniques and etc. The result of this study is as follows ; The basic concept of composition of plan is same as changing the axis of the plan in order to embody the Basilican space. But the inner elevation and detail of timber structure is different. Korean wooden churches were purely traditional timber structures, but Japanese wooden churches were pursued Western decorative detail by woodwork techniques in the capital, arch, rib, and vaulted ceiling. Japanese wooden church is more close to Western style church in the point of decoration and composition of inner space of church. There are different attitudes of naturalization of western church architecture in Korea and Japan.