The disputes between the military and the Department of State are the inner factors of U.S. government that influenced its policy to Taiwan between 1949 and 1950. In addition to their shared egoism, the different recognition of China is the primal reason which leads to the disputes. During this period, there are three-step development in U.S. government's policy to Taiwan: 1. sustaining the separate status of Taiwan from China (from December of 1948 to October of 1949); 2. the outsider period (from October of 1949 to February of 1950); 3. reconsidering its policy toward Taiwan (from February to June of 1950). During that period, US's policy to Taiwan was always based on reflecting on the status quo of China. Furthermore, in the process of decision making, both of military and the Department of State insisted on their own perspective options in the policy to Taiwan, and thus incurred great disputes between them. This article focuses on the "political dispute" by analyzing the U.S. government's policy to Taiwan between 1949 and 1950 and explicating the main reason that cause disputes between the military and the Department of State.