Over-exploitation of groundwater due to intensive irrigation and anticipated climate change pose severe threats to the water and food security worldwide, particularly in the North China Plain (NCP). Limited irrigation has been recognized as an effective way to improve crop water productivity and slow the rapid decline of groundwater levels. Whether optimized limited irrigation strategies could achieve a balance between groundwater pumping and grain production in the NCP under future climate change deserves further study. In this study, an improved Soil and Water Assessment Tool (SWAT) model was used to simulate climate change impacts on shallow groundwater levels and crop production under limited irrigation strategies to suggest optimal irrigation management practices under future climate conditions in the NCP. The simulations of eleven limited irrigation strategies for winter wheat with targeted irrigations at different growth stages and with irrigated or rainfed summer maize were compared with future business-as-usual management. Climate change impacts showed that mean wheat (maize) yield under adequate irrigation was expected to increase by 13.2% (4.9%) during the middle time period (2041–2070) and by 11.2% (4.6%) during the late time period (2071–2100) under three SSPs compared to the historical period (1971–2000). Mean decline rate of shallow groundwater level slowed by approximately 1 m a−1 during the entire future period (2041–2100) under three SSPs with a greater reduction for SSP5–8.5. The average contribution rate of future climate toward the balance of shallow groundwater pumping and replenishment was 62.9%. Based on the simulated crop yields and decline rate of shallow groundwater level under the future climate, the most appropriate limited irrigation was achieved by applying irrigation during the jointing stage of wheat with rainfed maize, which could achieve the groundwater recovery and sustainable food production.