Community health service institutions are the basic tentacles of medical services which directly indicates their relation to the quality and experience of health service.This paper focuses on the behavioral logic of community health service institutions under the background of new medical reform, and looks forward to a perspective on the grassroots practice caused by the reform of medical system through the behavioral analysis of the community health service institutions.The behavioral logic features of the community health service institutions were constructed based on the interview data Nanjing City using the grounded theory.It was found that the realization of public welfare orientation of the aforesaid institutions needs to be completed under the internal and external coordination.The degree of coordination among the interests, orientation, incentives and resource elements will determine the behavior orientation and basic operational practices in the community health service institutions.This study will provide a reference value for the cognition and optimization of healthcare reform policies.