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Objectives Our study aimed to examine whether the family doctor system can improve continuity of care for patients with diabetes. Design Registry-based, population-level longitudinal cohort study. Setting Linked data from the administrative Health Information System and the Health Insurance Claim Databases in a sample city in eastern China. Participants 30 451 insured patients who were diagnosed with diabetes before January 2015 in the sample city, with ≥2 outpatient visits per year during 2014–2017. Diabetics in the intervention group had been registered with family doctor teams from 2015 to 2017, while those who had not registered were taken as the control group. Interventions The family doctor system was established in China mainly to strengthen primary care and rebuild referral systems. Residents were encouraged to register with family doctors to obtain continuous health management especially for chronic disease management. Outcome measures Continuity of care was measured by the Continuity of Care Index (COCI), Usual Provider Continuity Score (UPCS) and Sequential Continuity of Care Index (SECON) in 2014–2017. Results COCI, UPCS and SECON of all diabetics in this study increased between 2014 and 2017. A difference-in-difference approach was applied to measure the net effect of the family doctor system on continuity of care. Our model controlled for demographic and socioeconomic characteristics, and severity of disease at baseline. Compared with the control group, diabetics registered with family doctors obtained an average 0.019 increase in COCI (SE 0.002) (p<0.01), a 0.016 increase in UPCS (SE 0.002) (p<0.01) and a 0.018 increase in SECON (SE 0.002) (p<0.01). Conclusion This study provides evidence that the family doctor system can effectively improve continuity of care for patients with diabetes, which has substantial policy implications for further primary care reform in China.