Background Family doctor contract service is an important service item in China’s primary care reform. This research was designed to evaluate the impact of the provision of family doctor contract services on the patient-perceived quality of primary care, and therefore give evidence-based policy suggestions. Methods This cross-sectional study of family doctor contract service policy was conducted in three pilot cities in the Pearl River Delta, South China,using a multistage stratified sampling method. The adapted Primary Care Assessment Tool-Adult Edition (PCAT-AS) was used to measure the quality of primary care services. Data was collected through face-to-face interviews held from July to November, 2015. Covariate analysis and multivariate Linear Regression were adopted to explore the effect of contract on the quality of primary care by controlling for the socio-demographic status and health care service utilization factors. Results A total of 828 valid questionnaires were collected. From the interviewees, 453 patients signed the contract (54.7%) and 375 did not (45.3%). Multivariate linear regression showed that patients who received services from contracted family doctors reported higher scores in dimensions of PCAT total score (β=-8.98, P<0.000), first contact-utilization(β=-0.71,P<0.001), first contact-accessibility(β=-1.49, P<0.001), continuity (β=1.27, P<0.001), coordination(referral) (β=-1.42, P<0.001), comprehensiveness(utilization) (β=-1.70, P<0.001), comprehensiveness(provision) (β=-0.99, P<0.001), family-centeredness(β=-0.52, P<0.01), community orientation(β=-1.78, P<0.001), than those who did not receive contract services after controlling socio-demographic and service utilization factors. There were no statistically significant differences in the dimensions of coordination (information system) (β=-0.25, P=0.137) and culture orientation (β=-0.264, P=0.056), than those who did not receive family doctor contract services. Conclusions This study demonstrates that the pilot implementation of family doctor contract services has significantly improved patients’ perceived primary care quality in the pilot cities, and could help solve the quality problem of primary care. It needs further promotion across the province.