Southeast Asia is a region where ethnic Chinese society has the longest history, the largest population and the prominent economic role in the world. In general, overseas ethnic Chinese lives in harmony with the indigenous people where they live. They have gradually integrated themselves with the mainstream society and have made contribution to the progress of the local society. But there are big differences in the integration of ethnic Chinese with the indigenous people in various countries because of the difference of the history in political, economic, social and cultural development. A comparison of Indonesia and Thailand in this aspect and its background is studied in this paper. Historically, the Dutch colonialists ruled Indonesia for more than 300 years, but Siam maintained the continuity of independence. This was the source of the contrast in the integration of ethnic Chinese with the mainstream society in Indonesia and Thailand. The analysis in this paper is made in two aspects. The first aspect covers the political and economic factors;the second aspect includes the social and cultural factors. This paper comes to the conclnsion that the contrast between the integration of ethnic Chinese with the mainstream society of Thailand and Indonesia was the result of the historical development of the two countries. In Southeast Asia the relation between ethnic Chinese and the native people is a part of the general problems of the society. The resolution of this part of the problem depends on the progress of the whole nation. The improvement of the relation between ethnic Chinese and indigenous people in Indonesia will mostly depend on whether the Indonesian economy is able to regain the high growth rates of the 1970s and whether the trend towards corporatization generated by such a growth has the effect of breaking down the lines of demarcation in economic live between ethnic Chinese and the native people there. Only if the social and political contradictions of Indonesia have been mitigated, economy growth has been achieved continuously,social stability has been brought about, great improvement has been made in living and education of native people, harmonious development can just be made between Chinese and native people.