Indo-Pacific, connected by water and the strait of Malacca, is home to human civilizations from time immemorial until recently. Nevertheless, Western civilization intervened and strongly influences the societies when the era of colonialism era begun. Hence, the societies are disrupted, and nation-states are created imitating what European colonial powers conveyed, especially one of the indigenous and most prominent civilizations such as Islam. Along with the rise of the Muslim population in the Indo-Pacific, Islam, as one of the remaining civilizations and Muslim society, has to strive in its native land to keep the rights upheld. This paper will examine the problematical condition that occurred after decolonization in Indo-Pacific, which Muslim society faced who live in the nation-state and being a minority at the same time. The phenomena of Euro-American centrism led the world to the recent phase and the rise of Muslims can contribute to globalizing International Relations (IR) by providing an alternatives international system in the post-colonial era. The paper will also emphasize the history of Asia as a significant momentum in IR discipline and any attempt to criticize the Euro-American centric model through the colonialism era in Indo-Pacific societies reaching post-colonial era by exhibiting examples in Muslim societies condition who struggle within its nation-state due to the absence of mutual understanding and the perpetuation of ethnopolitical conflict as the legacy of colonialism.