To restore groundwater levels and streamflow in the lower reach of the Tao’er River Basin, four water resources management measures were designed, including adjusting the reservoir discharge process, adjusting the surface-groundwater water supply ratio, implementing water diversion projects for groundwater recharge, and optimizing irrigation scheduling. The SWAT-MODFLOW model was used to simulate the water resources status of the watershed under single measures and different combinations of measures, analyze the response characteristics of groundwater level recovery degree, ecological flow satisfaction, and agricultural water supply guarantee rate to operation measures, and explore a suitable joint operation scheme for surface water and groundwater in the Tao’er River Basin. The results indicate that a single measure generally focuses on improving one indicator and is difficult to balance the other two. Different combinations of measures can effectively reduce runoff losses during the flood season while ensuring the ecological flow of rivers and agricultural water supply are not affected, thereby promoting the restoration of groundwater levels. In the historical scenario simulation from 1969 to 2016, compared with the current management plan of the basin, different combinations of measures achieved a 0.82 m increase in the average groundwater level of the overexploited area over the years, a 4.5% increase in ecological flow satisfaction at the outlet of the basin, and maintained an agricultural water supply guarantee rate of over 97.7%.