With the InVEST habitat quality model used to analyze the spatio-temporal variation characteristics of habitat quality in the Hongze Lake Basin from 1980 to 2020, the Johnes classical output coefficient model used to calculate pollution load output under different scenarios, and the regression model used to establish the relationship between pollution load and habitat quality, the effect of pollution load reduction measures on habitat quality was predicted. The results showed that the habitat quality deteriorated year by year in the Hongze Lake Basin, presenting a spatial pattern of south superior to north and east superior to west; the output of pollution load increased year by year, the pollution load had an obvious agglomeration effect in bad habitat quality areas, and there was a significant negative correlation between pollution load and habitat quality; under the condition of natural development (without reduction of pollution load), the average habitat quality in 2030 would further reduce by 1.0% to 2.4%, as compared with that in 2020; according to the watershed pollution load reduction target, the average habitat quality of the Hongze Lake Basin would increase by 0.9% to 2.2% in the scenario with the pollution load reduction rate of 8%, and the value would increase by 1.3% to 2.7% in the scenario with the pollution load reduction of 18%, as compared with the natural development scenario, demonstrating that pollution load reduction has significant effect on improving habitat quality.