Abstract: Based on the non-parametric method of double-output model, and on the basis of the measurement of cotton production efficiency of resources allocation, this article specifically researches the optimizing strategies for cotton production resources allocation configuration. The researching results show that the cotton production scale efficiencies of the major river basins are among the worst, which means that Central Government should further accelerate the transfer speed of surplus agricultural labor, rise farmland utilization efficiency, and make more efforts to eliminate the main constraining factors in China's cotton production efficiency. And according to the regional characteristics performed in the cotton production during the transferring period, the Central Government should stabilize Talimu River basin cotton production efficiency, further increase the cotton production resources allocation efficiency on Yangtze River Basin, and eliminate the Yellow River Basin inefficient cotton production situation.