Abstract: During the "Thirteenth Five-Year Plan" period, with the continuous deepening of ecological civilization reform, the water environment governance had been transformed into precise and scientific pollution control, and the water environmental quality had improved significantly. Based on the concept of multi-scale of time and space, a "multi-scale comprehensive evaluation" method was proposed to study the temporal and spatial evolution of surface water environmental quality. The surface water environmental quality in Chongqing City was the study object based on the data from national examination sections in the “13th Five-Year Plan”. Based on the environmental quality of the surface water and the variation law of the main pollutants in the time scale (annual and inner annual), we comprehensively analyzed the environmental quality from the point (entry and exit section) to the line (the main stream of the Yangtze River) to the surface (the surface water of the whole city) on the spatial scale. The results show that during the "13th Five-Year Plan" period, the environmental quality of surface water in Chongqing City national examination sections had improved step by year. The water quality in the second half of a year were generally better than those in the first half of a year. The concentration of major pollutants increased significantly in summer, and the surface water environmental pollution was mainly caused by agricultural non-point source pollution. The water quality in the whole region was negatively correlated with the level of economic development, as the water quality in eastern region was significantly better than that in the western region. The effects of nitrogen and phosphorus prevention and control were significant, with reduction rates of 30.89% and 10.45%.This result has practical significance for evaluating the effect of pollution prevention and control since the "13th Five-Year Plan", and also provides a theoretical basis for the implementation of related pollution control during the "14th Five-Year Plan".