The influence of religion in Southeast Asia is one of the most complicated matters, which the scholars cannot skip when they discuss the social issues in this region. In the history of Southeast Asia, Brahmanism, Buddhism, Islam and Catholicism have millions of followers in different nations. After the countries became independent, the religion conflicts occurred incessantly in the area where more than one religion existed. During 1960s and 1970s, the Muslim fought with Thai government in Patani, southern Thailand, because of tax and education. During 1970s and 1980s, the Muslim separatism brought a lot of trouble to Marcos government in Mindanao, southern Philippines, because of the land. In the end of 1990s, many people died in the conflict between the Christians and the Muslims in Ambon of Indonesia because of the political and economic turbulence. All these conflicts hurt the social development process in these countries.In this paper, the author analyzes the historic and systemic reasons of religious conflicts. The author considers that differences of religious beliefs are the superficial reason of the above-mentioned conflicts. Some secular interest conflicts perform through the religious form. Solving the conflict of interest is much more important than that of the conflict of religion.