China is in the process of integrating the new cooperative medical scheme (NCMS) and the urban residents’ basic medical insurance system (URBMI) into the urban and rural residents’ basic medical insurance system (URRBMI). However, how to integrate the financing policies of NCMS and URBMI has not been described in detail. This paper attempts to illustrate the differences between the financing mechanisms of NCMS and URBMI, to analyze financing inequity between urban and rural residents and to identify financing mechanisms for integrating urban and rural residents’ medical insurance systems.