To address the issues of both water resources allocation and sustainable management in agriculture areas with rising food demand, a simulation-optimization framework based on Flopy and Pymoo was proposed and developed for canal-well combined irrigation districts. The proposed framework first solved the many-objective water resources allocation problem which integrates groundwater simulation, crop production, and farmer income modules to quantitatively reveal the various trade-offs and synergies by using NSGA-III algorithm. The Entropy-TOPSIS method was then applied to recommend proper water allocation schemes. The proposed framework was further tested in Baojixia irrigation district considering various water supply and crop demand scenarios based on Copula-based uncertainty analysis. The Key findings are as follows: (1) the proposed framework could effectively optimize conjunctive water resources allocation problems of both surface water and groundwater; (2) low supply combined with high demand (p=0.17) is more likely to occur than high supply with high demand (p=0.02); (3) increased crop demand and restricted surface water negatively impact both water productivity and groundwater sustainability; and (4) the cumulative groundwater drawdown of recommend schemes is 36.9 % and 6.5 % higher under low to medium supply scenarios, while water productivity of recommend schemes decreases 28.2 % and 9.7 % with high and medium demand. This framework could provide useful insights for sustainable agricultural water management in canal-well combined irrigation district with various uncertainties in supply and demand scenarios.