BackgroundVillage clinic doctors (VCDs) are part of the health service force in rural China. VCDs’ job satisfaction (JS) is important to the stability of the three-tiered health service system. Since 2009, the Chinese government launched a new health care system reform (NHCSR) which affected VCDs significantly. This study aimed to analysing the effect of NHCSR on JS among VCDs.MethodsAll the data came from three surveys in Shandong Province conducted in 2012, 2015 and 2018. In 2012, an originally designed questionnaire was used to conduct a baseline survey of 405 VCDs from 27 townships in nine counties. In 2015 and 2018, 519 and 223 VCDs in the same counties were surveyed with the same questionnaire. Descriptive analysis and ANOVA were used to analyse the level and changes in VCDs’ JS.ResultsThe mean scores of VCDs’ total JS were 2.664 ± 1.069, 3.121 ± 0.931 and 2.676 ± 1.044 in 2012, 2015 and 2018, respectively, with a significant difference (F = 28.732, P < 0.001). The mean scores of the medical practice environment and the job itself showed a continuous downward trend. The trends of the mean scores for job reward, internal work environment and organizational management were consistent with the trend for total JS.ConclusionThe NHCSR had a partly negative impact on VCDs’ JS. Policy-makers should pay more attention to VCDs’ job reward and medical practice environment. With the implementation of new reform policies, VCDs’ JS should be the subject of more systematic and detailed research.