Stroke has always been a severe disease and imposed heavy financial burden on the health system. Equity in patients in regard to healthcare utilization and medical costs are recognized as a significant factor influencing medical quality and health system responsiveness. The aim of this study is to understand the equity in stroke patients concerning medical costs and healthcare utilization, as well as identify potential factors contributing to geographic variation in stroke patients' healthcare utilization and costs. Covering 31 provinces in mainland China, our main data were a 5% random sample of stroke claims from Urban Employees Basic Medical Insurance (UEBMI) and Urban Residents Basic Medical Insurance (URBMI) from 2013 to 2016. The Theil index was employed to evaluate the equity in stroke patients in regard to healthcare utilization and medical costs, and the random-effect panel model was used to explore the impact of province-level factors (health resource factors, enabling factors, and economic factors) on medical costs and health care utilization. Stroke patients' healthcare utilization and medical costs showed significant differences both within and between regions. The UEBMI scheme had an overall lower Theil index value than the URBMI scheme. The intra-region Theil index value was higher than the inter-region Theil index, with the Theil index highest within eastern China, China's richest and most developed region. Health resource factors and enabling factors (represented by reimbursement rate and education attainment years) were identified significantly associated with medical costs (P < 0.05), but have no impact on average length of stay. China's fragmented urban health insurance schemes require further reform to ensure better equity in healthcare utilization and medical costs for stroke patients. Improving education attainment, offering equal access to healthcare, allocating health resources reasonably and balancing health services prices in different regions also count.