The paper generalized Malian river basin into five water resources partitions and used index analysis method to predict water supply and demand and carry out balance analysis in 2020 and 2030.Then it utilized improved decision tree method to conducted risk analysis,and introducted expert consulting probabilities into the sensitivity analysis of decision tree, finally it recommended the allocation scheme of water supply and demand 2020 and 2030. The paper used the theory of system analysis and optimization technology to build the large system of the basin and multi-objective water resources optimal allocation model,and used the optimized NSGA-II method to solve problem and obtained the optimal allocation scheme under the recommended plan of water allocation in 2030. Finally according to the optimal allocation scheme and forecasted water demand to conduct balance analysis, which obtained that under the condition of optimal water allocation scheme and the forecasted water requirement. The optimal allocation scheme achieved the most optimal water distribution and made the precious and limited water resources produce the maximum social, economic and environmental benefits and provide water resources support for the rapid growth of economic and energy industry in Malian river basin.