Abstract: A new method, projection pursuit based on genetic algorithm, was used to evaluate agricultural water use efficiency for solving the incompatibility of evaluation indexes of it. Projection pursuit can be used to project high dimensional data to low dimensional space and find the optimum projection vector of data in one-dimensional space, which is helpful to comprehensively evaluate the value and direction of every index in comprehensive evaluation. The projection index value was given by multiplying projection vector by standardization value of evaluation indexes, which can synthesize the characteristics of agricultural water use efficiency and classify agricultural water use efficiency. The method was used to comprehensively evaluate eighty-one county units in Gansu Province, and the results of the value and direction of every index were accorded with the practice. The comprehensive use efficiencies of agricultural water of eighty-one counties were given.