Accurate and up-to-date provincial and regional-level stroke prevalence estimates are important for research planning and targeted strategies for stroke prevention and management. However, recent and comprehensive evaluation is lacking over the past 30 years in China. This study aimed to examine the geographical variations in stroke prevalence based on data from the National Epidemiological Survey of Stroke in China (NESS-China) and demonstrate urban-rural transition and trend over three decades. The stroke prevalence (prevalence day, August 31, 2013) was estimated using the world standard population. The stroke prevalence was 873.4 per 100,000 population, and varied from 218.0 in Sichuan to 1768.9 in Heilongjiang. Stroke prevalence exhibited a noticeable north-south gradient (1097.1, 917.7, and 619.4 in the north, middle, and the south, respectively; P < 0.001) and showed a 2.0-fold, 1.5-fold, and 1.2-fold increase in rural areas in the north, the middle, and the south, respectively, from 1985 to 2013. Overall, stroke prevalence was higher in the rural regions than in the urban (945.4 versus 797.5, P < 0.001) regions. However, the converse was depicted in 12 provinces. A noticeable geographical variation in stroke prevalence was observed and was evolving overtime in China. It is imperative that effective public health policies and interventions be implemented, especially in those regions with higher prevalence.