Background The New Cooperative Medical Scheme (NCMS) is a social health insurance available to rural Chinese residents. Over time, several concerns to this system have been raised, including disparities among healthcare utilization and expenditures. Most studies only discuss disparities in general in NCMS, with few studies concentrating on comparing disparities between urban and rural regions. Moreover, this issue has an increasing importance due to the rapid population growth of rural migrants. Therefore, we conducted our study to explore urban and rural disparities among NCMS beneficiaries.Methods Our study is based on Chinese Health and Retirement Longitudinal Study (CHARLS) for 2015. Our targeted sample is individuals with rural hukou and only covered by NCMS. We define and use influential factors in our logistic regressions and descriptive tables to compare urban and rural disparities among these NCMS beneficiaries. Results In terms of inpatient care, urban beneficiaries have a lower probability (OR=1.013, P=0.892) and frequency (1.39 vs. 1.47, P=0.131) of having an inpatient visit than rural beneficiaries. However, urban beneficiaries have higher out-of-pocket (OOP) expenditures among inpatient visit (¥6788.98 vs. ¥6163.92, P=0.470) and medicine (¥3907.30 vs. ¥2649.67, P<0.01). In addition, urban beneficiaries were found to have higher reimbursement of inpatient visit (¥4457.66 vs. ¥4127.83, P<0.001) and medicine (¥2466.93 vs. ¥1774.55, P<0.05). In terms of outpatient care, urban beneficiaries have less possibility (OR=1.074, P=0.384) and frequency (2.15 vs. 2.26, P=0.225) of an outpatient visit than rural beneficiaries. Moreover, compared to rural beneficiaries, urban beneficiaries have less out-of-pocket (OOP) expenditures of outpatient visit (¥709.80 vs. ¥ 710.98, P=0.608) and drugs (¥448.68 vs. ¥ 522.95, P=0.645), and less reimbursement of outpatient visit (¥296.03 vs. ¥ 344.51, P=0.808) and drugs (¥99.25 vs. ¥ 114.60, P<0.05).Conclusion In terms of healthcare utilization, rural beneficiaries have both higher probability and frequency of inpatient and outpatient visits. In terms of healthcare expenditures, urban beneficiaries get more inpatient reimbursement with higher inpatient expenditures, while rural beneficiaries get more outpatient reimbursement with higher outpatient expenditures. Both situations have not solid answer yet, and therefore require further research.