The purpose of the study is to analyze the impact factors and the path of Japan’s FTA strategy by a qualitative choice model depending on the data in 1997. Combined with the practice of Japan’s FTA strategy and models’results, the roadmap of Japan’s FTA strategy in the future has been empirically predicted. Our conclusion reveals that although Japan’s FTA Strategy shows different features and focuses in different periods, factors such as geographical distance, the difference of factor endowment, trade complementarityand trade integration degree between Japan and its partners have always worked as the essential causes which affect Japan’s option for its FTA partners in the long term. The empirical model correctly predicts 94% of the 51 Japan’s FTAs in 54 existing in 2014 and 90% of the remaining 85 no FTA pairs in 94.