Based on a comprehensive analysis of the source region as well as genetic process and tectonic setting of this intrusion, in combination with the regional geological data, it is held that Muztagata intrusion was most likely derived from partial melting of basaltic rocks in the lower crust under the condition of high temperature (>839.6℃) and low pressure (<15 kbar) in the transitional period from primary collision to post-collision, and subsequently it underwent the crystallization of plagioclase, apatite and ilmenite together with the injection of mantle-derived magma. In addition, the Western Kunlun granites had the evolutionary characteristic of conversion from I-type to A-type granite during the post-collision of Paleo-Tethys.