Although groundwater is the primary drinking water source in northern of China, little is known about generation mechanisms and related health risks of high fluoride groundwater at the geomorphic transition zones. Thus, 419 groundwater samples were collected from Zhangjiakou region, where is a typically geomorphic transition zone of the North China Plain and the Inner Mongolia Plateau, to conduct the hydrochemical analysis, geochemical modeling, multivariate statistical analysis, and health risks assessment. From the results, F− concentration in groundwater had a range of 0.05–9.71 mg L−1. About 37.1% and 26.2% of groundwater samples from Bashang region (BSR) and Baxia region (BXR), respectively, were over the 1.50 mg L−1, which were mainly distributed in the groundwater flow retardation area and/or evaporation discharge area. Thermodynamic simulations demonstrated that F-bearing minerals dissolution and Ca2+/Mg2+ removal via calcite/dolomite precipitation primarily governed high-F- groundwater formation in the whole study area. Competitive adsorption, evaporation, evaporites dissolution and salt-effect also affected F− enrichment in BSR. Desorption in alkaline environment, ion exchange and human activities played a vital role in F− enrichment at BXR. The multivariate statistical analysis revealed that the origin of F− contamination was geogenic in BSR; whereas, it was geogenic and anthropogenic in BXR. Besides, more than 71.8%, 51.0%, 36.1% and 25.5% of the study area exceeded the acceptable level (health index>1) for infants, children, adult males, and females, respectively. The health risks for different groups of people varied significantly and ranked: infants > children > males > females, suggesting that younger people were more susceptible to fluoride contamination. Meanwhile, females were more resistant to fluoride contamination than males. These findings are vital to providing insights on high-F- groundwater formation, investigate the situation of health risks, and conduct the integrated management for high fluoride groundwater in geomorphic transition zones at northern China.