Objectives: To assess the service system operating efficiency of Basic Healthcare Facilities of Areas of primary care comprehensive reform. Methods: The data of China Health Statistical Yearbook of areas of primary care comprehensive reform from 2013 to 2015 was used to analyze annual growth rate of average daily outpatient and emergency visits and inpatients per doctor, and the number of chronic patients (Hypertensive and diabetic patients) and older people managed by each medical staff. DEA-BCC model and Malmquist model were applied to perform analysis. Results: The annual increasing rate of average daily outpatient and emergency visits and inpatients per doctor were respectively 4.3% and 0.5% from 2013 to 2015.The annual growth rate of the number of chronic patients and older people managed by each medical staff were respectively 0.8%. and -4.3%. In 2015, 48.3% of the district’’’’’’’’s community health service institutions and 63.0% of the township hospitals were in a relatively effective operational state. Compared with 2014, These districts and counties which primary care mechanism reform and innovation efforts, the total factor production efficiency were improved. The total factor productivity of community health services and township hospitals decreased by 5.2% and 1.0% from 2013 to 2015. Conclusions: There is still big room improvement of the operating efficiency of Primary health care institutions. In this sense, we need to make up the technical shortcomings，continue to improve the comprehensive reform of primary health care, improve the overall operational efficiency.