Objective To analyze the fairness and impact mechanisms of the allocation of public health physician resources in China. Methods The fairness of public health physician resource allocation in 31 provinces across the country was set as the outcome variable, and 7 indicators were selected from the government, socio-economic and individual levels as conditional variables, and a fuzzy set qualitative comparative analysis (fsQCA) was performed. Results There were large differences in the allocation of public health physician resources in 31 provinces in China. Single factors cannot constitute a necessary condition to affect the fair allocation of public health physician resources. There were 10 paths that affect the fair allocation of public health physician resources, of which 2 paths had high fairness configurations, with an overall consistency of 0.97 and an overall coverage of 0.61. There were 8 paths in low fairness configurations, with an overall consistency of 0.96 and an overall coverage of 0.83. Conclusion Population aggregation is the basic premise for determining the fair allocation of public health physician resources. Financial support and residents’ income are key guarantees to support the fair allocation of public health physician resources. Medical insurance and basic public health service subsidies are complementary support for promoting the fair allocation of public health physician resources. Multi-factor coupling is a systematic mechanism for realizing the fair allocation of public health physician resources.