A quantitative control model of ecological environment non-point source pollution load considering storm runoff was proposed. According to the positive index of pollution source, the pollution load reduction space of non-point source was optimized, the pollution load control target model was established, and the optimal pollution load quantitative control scheme was obtained by using genetic algorithm. Taking Dulan area of eastern Qaidam Basin as a case, the control performance of the proposed method was tested. The comparative experiment results before and after pollution load control show that: The average concentration of pollutants decreases from 0.035mg/L to 0.012mg/L, the average reduction rate reaches 65.7%; the peak concentration decreases from 0.078mg/L to 0.018mg/L, and the maximum reduction rate reaches 88.2%. The results could provide theoretical basis for the efficient utilization of water resources, water ecological protection and regional water resources planning and utilization in Qaidam Basin, and data support for the ecological environment management project in this region.