Background: Family doctors can fulfill the gatekeeper duty to protect the residents' health, which depends on their work competency and stability. The study aimed to identify factors influencing work competency and stability among Shanghai family doctors. Methods: This study was a 2-year follow-up survey (2013/2016). A representative sample of 146 family doctors in Shanghai community health service centers was interviewed in 2013. The tracked sample (n = 142) was resurveyed in 2016. A 50-item questionnaire organized into four parts, i.e., general demographic characteristics, working conditions, cognition about family doctor services, and job satisfaction was issued to all family doctors. Models for factors influencing family doctors' work competency and stability were then established. The collected data were analyzed using ordinal regression methods and descriptive, factor, and multiple-factor analyses. Results: The family doctors' work competency model showed demographic characteristics (education level and job title), family doctors' team, family doctors' training, grasp of specific content regarding the family doctor system, and whether the family doctors' ability was played and demonstrated were statistically significant at different levels (P < 0.05). The analysis of family doctors' work stability showed that work competency (whether it was possible to provide residents with all contents specified in the contract service package, employment form, and support satisfaction) and work cognition (whether the daily work was meaningful and had value) had a significant impact on work stability (P < 0.05). Conclusion: Family doctors' job satisfaction is a key factor affecting their work stability. Family doctors' competency can also affect their job stability, and their work cognition may play a role in work competency and stability. This study provides evidence for strengthening the stability of the family doctor teams in Shanghai.