Controlled drainage (CD) has emerged as an effective strategy to prevent field waterlogging and mitigate drought during crop growth by altering the hydrological process, while few studies have quantified its effect on groundwater-surface water interactions and groundwater recharge at a regional scale. In this study, a new model is developed for the coupled numerical simulation of water flow in ditches, soil, and underground aquifers under CD conditions. The domain is partitioned into horizontal sub-areas and two vertical layers, with ditches discretized into segments based on groundwater flow grids. The Saint-Venant equations, Richards equation, and MODFLOW are applied to describe water movement processes in ditches, soil, and underground aquifers, respectively. The proposed model is calibrated and validated using five years of observations of ditch water levels (DWL) and groundwater levels, demonstrating excellent agreement with observed data. Subsequently, water balance components of the shallow aquifer below 1 m depth (GW), 1 m of root layer soil profile (SW), and ditch water (DW) under seven scenarios with different control schemes during flood and dry seasons are analyzed to quantify variations in hydrological processes caused by CD. The results show that CD significantly impacts water within SW, GW, and DW, soil evaporation, infiltration, and net recharge from GW to SW (GtoS) by altering regional groundwater table depth (GWT) through the exchange between DW and GW (DtoG and GtoD). GWT and DW show moderate correlation with GtoD, while their correlation with DtoG varies significantly under different rainfall conditions. Smaller precipitation results that precipitation and GWT have a higher linear correlation with water balance components during the dry season compared to the flood season. The correlation values (r) between transpiration (T) and GWT range from −0.99 to 0.96 and −1 to −0.85 during the flood and dry seasons, respectively, indicating a pronounced influence of CD on crop growth. On average, a 1 m increase in DWL control scheme leads to a 0.51 m increase in DWL, and regional GWT decreases by 0.35 m and 0.24 m during flood and dry seasons, respectively. Furthermore, for every 1 m decrease in GWT, net GtoS increases by 36.1 mm and 28.1 mm, respectively, resulting in an increase in SW by 13.9 mm and 11.8 mm, respectively. Considering the varying main crop water stress and the impact of CD under different rainfall conditions, an appropriate CD scheme needs to be adjusted accordingly. These findings provide a quantitative reference for the effect of CD on regional hydrological process and serve as a typical case for similar areas aiming to implement CD strategies for waterlogging and drought control.