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  For some challenges about water trade price,water-saving coefficients,approach and so on in application of multi-objective model for optimal allocation of water resources with two-story structure,this paper puts forward the solution to the bi-level programming model of the optimal allocation of water resources,which assigns values about water trade price of and coefficient of water-saving via random-points in a certain range,and applies genetic algorithm to solve the upper-story programming,and uses simplex method to solve the lower-story programming.It Comparative studies solution and application from solution ideas,method design,calculation results,and so on,and puts forward some challenging issues for study.……