BackgroundChina’s primary health care system has undergone major changes since the new round of medical reform in 2009, but the current status of primary health care institution service efficiency is still unsatisfactory. The purpose of this study is to compare and evaluate the China’s primary health care institution service efficiency and provide a reference for improving the efficiency and promoting the development of primary health care institution.MethodsBased on panel data of 31 provinces (municipalities directly under the central government and autonomous regions) in mainland China from 2011 to 2020, using the super efficiency slack-based measure-data envelopment analysis model, to analyze the data from a static perspective, and the changes in the efficiency of primary health care services were analyzed from a dynamic perspective by using the Malmquist index method. Spatial autocorrelation analysis method was used to verify the spatial correlation of primary health care service efficiency among various regions.ResultsThe number of Primary health care institutions increased from 918,000 in 2011 to 970,000 in 2020. The average primary health care institution service efficiency in the northeastern region including Jilin (0.324), Heilongjiang (0.460), Liaoning (0.453) and northern regions such as Shaanxi (0.344) and Neimenggu (0.403) was at a low level, while the eastern coastal regions such as Guangdong (1.116), Zhejiang (1.211), Shanghai (1.402) have higher average service efficiency levels. The global Moran’s I showed the existence of spatial autocorrelation, and the local Moran’s I index suggested that the problem of uneven regional development was prominent, showing a contiguous regional distribution pattern. Among them, H–H (high-efficiency regions) were mainly concentrated in Jiangsu, Anhui and Shanghai, and L-L regions (low-efficiency regions) were mostly in northern and northeastern China.ConclusionThe service efficiency of primary health care institution in China showed a rising trend in general, but the overall average efficiency was still at a low level, and there were significant geographical differences, which showed a spatial distribution of “high in the east and low in the west, high in the south and low in the north”. The northwestern region, after receiving relevant support, has seen a rapid development of primary health care, and its efficiency was steadily improving and gradually reaching a high level. The average primary health care institution service efficiency in the northeastern region including the northern region of China was at a low level, while the average efficiency in the eastern coastal region and some economically developed regions was high, which also verifies the dependence and high symbiosis of primary health care institution service efficiency on regional economy.