This article focuses on the discussion of the territorial factors, geo-politics, great powers relations and related issues in the Indonesia-Malaysia political relations during the period 1961-1971. The territorial factor and geo-politics were among the vital factors in the Indonesia-Malaysia political relations and great power relations in the South East Asia Region. It had a close relationship with the economic factor, idiosyncratic and ideological conflict. Both sides of the hegemonic (the U.S.) and counter-hegemonic power (the Soviet Union) were involved in the Indonesia-Malaysia conflict. The geographical position of Indonesia's and Malaysia's territory was vital for both sides of the great powers (and also for China Communists). Hence, the discussion and analysis of the territorial factor had a close relationship with the geo-politics, international ideological factors, economics and idiosyncratic factors. The changes in ideological development, economic situation, changes in leadership and changes in systemic power configuration affected the territorial factor. The changes in the above mentioned factors during the period before and after 1965 in Indonesia had a great impact upon the territorial issue and the political relations of Indonesia-Malaysia and great powers relations in the South East Asian Region.