The integration of Southeast Asia has reached a crucial moment after half a century’s development. The building of ASEAN community attracts attentions and participations of countries inside and outside the region including Japan. Japan has played a positive role in the process of the integration of Southeast Asia. However，due to the contradictory between Japanese special identity and its purse in the postwar era，and that between its US policy and regional cooperation，Japan has certain cognitive bias in perceiving the integration of Southeast Asia，which has resulted in the swinging of its Southeast Asia diplomacy from implementing the diplomacy highly dependent on U.S. to following the trend of Asia Pacific integration，getting Japan trapped in contradiction and dilemma. Japanese regional policy，on the basis of seeking for partnership and forming factions in AESAN according its own interest，is harmful to cooperation in the East Asia and the Asia Pacific region，becoming a major challenge in the process of China’s peaceful rise.