The human activities and urbanization process have changed the underlying surface of urban areas, which would affect the recharge of groundwater through rainfall infiltration and may further influence the groundwater environment. Accordingly, it is imperative to investigate the variation of hydrological cycle under the condition of underlying surface change. Based on the high-precision remote sensing data of 2000, 2005, 2010 and 2015, and Soil and Water Assessment Tool (SWAT) model, this work firstly studied the land use change and the corresponding changes in runoff generation mechanism and rainfall infiltration coefficient in Su-Mi-Huai area, Beijing, China. Meanwhile, SWAT-MODFLOW semi-loose coupling model was applied to analyze the water balance in the study area in typical hydrological years. The results showed that the area of the construction land (urban and rural residential land) increased by 1.04 times from 2000 to 2015, which is mainly attributed to the conversion of cultivated land to construction land in the plain area. This change caused the runoff in the area to increase by 7 × 10⁶ m³, the runoff coefficient increased by 17.9%, and the precipitation infiltration coefficient was less than the empirical value determined by lithology. Compared with 2000, the average annual precipitation infiltration coefficient in 2018 decreased by 6.5%. Under the influence of urbanization process, the maximum reduction rate of precipitation infiltration recharge is up to 38%. The study investigated the response of surface runoff and precipitation infiltration recharge to land use change, which can provide helps for water resources managers to coordinate the relationship between land use change and rational water resources planning.