Previous studies which have shown the existence of gender disparities in hypertension risks often failed to take into account the participants’ spatial and temporal information. In this study, we explored the spatio-temporal variation for gender-specific hypertension risks in not only single-disease settings but also multiple-disease settings. From the longitudinal data of the China Health and Nutrition Survey (CHNS), 70,374 records of 21,006 individuals aged 12 years and over were selected for this study. Bayesian B-spline techniques along with the Besag, York, and Mollie (BYM) model and the Shared Component Model (SCM) model were then used to construct the spatio-temporal models. Our study found that the prevalence of hypertension in China increased from 11.7% to 34.5% during 1991 and 2015, with a higher rate in males than that in females. Moreover, hypertension was found mainly clustered in spatially adjacent regions, with a significant high-risk pattern in Eastern and Central China while a low-risk pattern in Western China, especially for males. The spatio-temporal variation of hypertension risks was associated with regional covariates, such as age, overweight, alcohol consumption, and smoking, with similar effects of age shared by both genders whereas gender-specific effects for other covariates. Thus, gender-specific hypertension prevention and control should be emphasized in the future in China, especially for the elderly population, overweight population, and females with a history of alcohol consumption and smoking who live in Eastern China and Central China.