Primary care physicians and their teams are the leading force in constructing primary medical services, undertaking the critical responsibility of residents' essential health, and also related to realizing the national health goal. However, primary care physicians generally have a high turnover rate due to problems such as high work pressure, low salary levels, and limited career development. Therefore, exploring primary care physicians' resignation intentions plays a vital role in promoting the construction of primary care physicians' health service system. This study explores the factors influencing the resignation intentions of primary care physicians, specifically examining the roles of work-family conflict, job satisfaction, professional identity, and emotional exhaustion. By understanding these dynamics, the research aims to inform strategies that can enhance the stability and effectiveness of primary care services, ultimately contributing to the improvement of public health infrastructure and achieving national health goals. This investigation will utilize structural equation modeling to analyze the interrelationships among the identified variables, thereby providing a comprehensive framework for addressing the high turnover rates among primary care physicians. This study uses the work-family conflict, job satisfaction, professional identity, and emotional exhaustion scales. The data comes from a cross-sectional survey in Zhejiang Province, China, in 2022. Using SPSS 27 and Mplus8.3 software to analyze 1205 primary care physicians and their team members, the selected cases all answered the relevant questions of resignation intention. The potential relationship among work-family conflict, job satisfaction, professional identity, emotional exhaustion, and family doctor resignation intention was explored by constructing structural equations. Work-family conflict can directly and positively affect primary care physicians' resignation intention (β = -0.546, p < 0.001). The results of the mediation model found that job satisfaction, professional identity, and emotional exhaustion were significantly related to work-family conflict, and primary care physicians' resignation intention has a significant mediating effect. It mainly includes six intermediary approaches: one is through the independent intermediary effect of job satisfaction; the second is through the independent intermediary effect of professional identity; the third is through the chain intermediary effect between Job satisfaction and professional identity; the fourth is through the intermediary effect of Job satisfaction and emotional exhaustion chain intermediary; fifth is through the chain intermediary of professional identity and emotional exhaustion; sixth is through the complex chain intermediary of job satisfaction, professional identity, and emotional exhaustion. Primary care physicians have a high score in resignation intention, which deserves continuous attention. Relevant department can help primary care physicians balance work and family roles, provide them with appropriate resources and rewards, as well as a good working environment and career development opportunities, to improve their job satisfaction and professional identity and reduce emotional exhaustion, thereby reducing the risk of resignation intention.