Background: Despite improvement in health outcomes over the past few decades, China still experiences striking rural-urban health inequalities. There is limited research on the rural-urban differences in health system performance in China. Method: We conducted a cross-sectional analysis to compare health system performance between rural and urban areas in five key domains of the health system: effectiveness, cost, access, patient-centredness and equity, using data from the WHO Study on Global AGEing and adult health (SAGE), China. Multiple logistic and linear regression models were used to assess the first four domains, adjusting for individual characteristics, and a relative index of inequality (RII) was used to measure the equity domain. Findings: Compared to urban areas, rural areas had poorer performance in the management and control of hypertension and diabetes, with more than 50% lower odds of having breast (AOR = 0.44; 95% CI: 0.30, 0.64) and cervical cancer screening (AOR = 0.49; 95% CI: 0.29, 0.83). There was better performance in rural areas in the patient-centredness domain, with more than twice higher odds of getting prompt attention, respect, clarity of the communication with health provider and involvement in decision making of the treatment in inpatient care (AOR = 2.56, 2.15, 2.28, 2.28). Although rural residents incurred relatively less out-of-pocket expenditures (OOPE) for outpatient and inpatient services than urban residents, they were more likely to incur catastrophic expenditures on health (AOR = 1.30; 95% CI 1.16, 1.44). Wealth inequality was found in many indicators related to the effectiveness, costs and access domains in both rural and urban areas. Rural areas had greater inequalities in the management of hypertension and coverage of cervical cancer (RII = 7.45 vs 1.64). Conclusion: Our findings suggest that urban areas have achieved better prevention and management of noncommunicable disease than rural areas, but access to healthcare was equivalent. A better understanding of the causes of the observed variations is needed to develop appropriate policy interventions which address these disparities.