Background There is a paucity of evidence regarding the definition of the quality of primary healthcare (PHC) in China. This study aims to develop a modified conceptual framework PHC quality based on the context of rural China and evaluate the PHC quality for chronic diseases in rural areas. Methods This mixed-methods study, involving a patient survey, a provider survey and chart abstraction, and second-hand registered data, was set in three low-resource counties in rural China from 2021 to 2022. Rural patients with hypertension or type 2 diabetes, health care workers providing care on hypertension or diabetes were involved. Standardized PHC quality score was generated by arithmetic means or Rasch models of Item Response Theory. Results A modified PHC quality framework was presented. High-quality PHC for chronic diseases encompasses three core domains: a competent PHC system (comprehensiveness, accessibility, continuity, and coordination), effective clinical care (assessment, diagnosis, treatment, disease management, and provider competence), and positive user experience (information sharing, shared decision-making, respect for patients’ preferences, and family-centeredness). This study included 1355 patients, 333 healthcare providers and 2203 medical records. Ranging from 0 (the worst) to 1 (the best), the average quality score for PHC system was 0.718, with 0.887 for comprehensiveness, 0.781 for accessibility, 0.489 for continuity, 0.714 for coordination. For clinical care, average quality was 0.773 for disease assessment, 0.768 for diagnosis, 0.677 for treatment, 0.777 for disease management, and 0.314 for provider competence. The average quality for user experience was 0.727, with 0.933 for information sharing, 0.657 for shared decision-making, 0.936 for respect for patients’ preferences, and 0.382 for family-centeredness. The differences in quality among population subgroups, although statistically significant, were small. Conclusion The PHC quality in rural China has showed strengths and limitations. We identified large gaps in continuity of care, treatment, provider competence, family-centeredness, and shared decision-making. Policymakers should invest more effort in addressing these gaps to improve PHC quality.