Providing long-term primary health care services and certain specialist services to patients with chronic diseases through hospital-community healthcare centers’ service collaboration is the main strategy for the health service system to cope with chronic diseases. The series of extra costs resulted from the hospital-community healthcare centers’ service collaboration system has become a matter of concern. The Transaction Cost Theory provides a clear analytical framework for examining the costs of the new medical system. This paper will point out difficulties that the hospital-community healthcare centers’ chronic disease medical service collaboration is facing in current stage, review the development of Transaction Cost Theory and its application in health field, and put forward a measurement method from dimensions of health administrative departments, health care providers and patients. This paper may enlighten the optimization of hospital-community healthcare centers’ chronic disease medical service collaboration system.