Aim: To provide a framework for provider payment reform for primary care physicians in China. Background: Primary health care is central to health system reform and payment incentives have significant consequences for the equity and efficiency of it. Methods: This paper describes the special payments system for public primary health institutions and the subsequent internal salary remuneration to primary care physicians in China. Based on an analysis of the major challenges, we suggest a reform framework including the pattern of governance, and payments to primary health institutions and employed physicians. Findings: A mixed system of input-based and output-based payments to institutions would probably be appropriate under a long-term and relational contract with the government. It was also advised that internal remuneration is provided by a basic salary plus a bonus based on performance, and an extra-regional allowance. We hope that the results can be used to shift the passive budgeting of in-house staff within the public primary health institutions toward strategic purchasing.