The global war on terror that was started after 11/9 tragedy has continued until to date. The global war on terror not only shaped the new political balance in the international world, but also influenced the relationships between the U.S. and Western countries with Muslims countries and Muslims around the world. This is because the war on terror has positioned Islam and Muslims in negative image as the serious threat to the West. Many people stated that the 11/9 tragedy is the evidence of “the clash of civilizations” between Islam and the West. As a result, some observers argue that the war on terror is the war against Islam based on the clash of civilizations thesis. However , others rebut this argument by explaining the facts that many Islamic countries supported to the war on terror . In fact, Islam has many schools of thought and cannot be understood in single understanding. Importantly , Islamic extremist movements are not the mainstream group in Muslims societies. This article will examine the relationship between the war on terror and the clash of civilizations thesis. It also assesses the Islamic world and Muslims response toward this agenda. It will argue that the war on terror is not war against Islam, but the war against terrorist groups and radical Muslims which often hijacked Islam.