Background: There has been great shortage of primary care physicians (PCPs) in China, especially in western areas. Job satisfaction plays a great role in retaining people. The aim of this study is to investigate the job satisfaction of PCPs and associated factors in 11 provinces of western China, thus providing necessary reference values for stabilizing the primary care workforce and improving the quality of primary care services. Method: A sample of 2103 PCPs working in western China were surveyed using a stratified, multistage and random sampling method in 2011. The characteristics of participants were recorded by a structured questionnaire. A multilevel model (MLM) and quantile regression (QR) were applied to assess the association between job satisfaction and possible risk factors. Results: Of the 2103 doctors surveyed, the overall satisfaction score was 3.26 ± 0.68 (from 1 to 5). MLM indicated that age group, income satisfaction, unit policy approval, personal planning, career attitude, work value and patient recognition were positively correlated with job satisfaction, while turnover intention was negatively correlated with job satisfaction. QR were not completely consistent with MLM and further explored the differences in different job satisfaction score percentiles on each domains. Conclusion: This study showed that the job satisfaction of PCPs in western China was not high. The MLM and QR discussed were not entirely consistent, the latter one provided more information and robust results. Measures should be taken in streamlining administration and institute decentralization, creating more opportunities for additional training, raising PCPs’ income, improving the social status of doctors and improving the relationship between doctors and patients.