Background and Purpose As a leading cause of disability and death in China, stroke as well as its epidemiologic features have gained increasing attention. Prior studies, however, have overgeneralized the north-to-south gradient in China. Whether the differences exist across urban and rural areas remains unexplored. This study therefore aims to investigate the north-to-south gradient in stroke incidence across urban and rural China. Methods The present prospective cohort study analyzed data from the China Health and Nutrition Survey 1997 to 2015. By including 16,917 individuals from diverse social contexts, we calculated the age-standardized incidence of stroke across regions and the age-adjusted risk ratio (aRR). Cox proportional hazards models with time-varying covariates were employed to analyze variations in incident stroke. Results During the follow-up, age-standardized incidence of stroke ranged from 4.17 per 1,000 person-years (95% confidence interval [CI], 3.38 to 4.96) in the north region to 1.95 (95% CI, 1.60 to 2.30) in the south region (aRR, 2.04; 95% CI, 1.58 to 2.64; P<0.001). The north-to-south gradient of stroke incidence was observed only in rural areas, but not in urban areas. Hierarchical modelling analyses further indicated that the regional differences could be mostly explained by the disparities in the prevalence of hypertension. Conclusions The present study extends the current evidence on the north-to-south gradient by demonstrating that the difference varied across urban and rural China. Our findings highlight the importance of hypertension management as the measure for alleviating regional differences in stroke incidence.