The Danjiang River Basin (Henan Section) is the water source of the Middle Route of the South-to- North Water Transfer Project. Its ecological environment quality has received increasing attention. In this study, on the basis of the ecological environment of the study area, we constructed the evaluation index system from four aspects: ecological basis, ecological structure, ecological stress and ecological benefits. The variable fuzzy set model was improved by using the central point triangle whitening weight function and the relative difference function. The ecological environment quality of the Danjiang River Basin (Henan Section) in the past 20 years was evaluated, and the evolution patterns and causes of ecological environment quality were analyzed by combination with land use changing. And the results showed that the area with better ecological environment quality was significantly larger than the deterioration area. The area with poorer grade was decreased from 441.22 km² in 1998 to 3.93 km² in 2017, and its proportion was correspondingly decreased from 2.23% to 0.05%. The area with the ordinary grade was decreased from 4528.79 km² in 1998 to 2636.47 km² in 2017, and its proportion was correspondingly decreased from 53.67% to 31.24%; The moderately graded area was increased from 3132.7 km² in 1998 to 5206.88 km² in 2017, and its proportion was increased from 37.12% to 61.71%; the area with good grade was increased from 319.58 km² in 1998 to 579.01 km² in 2017, the area with the excellent grade of an evaluation rating was almost unchanged. Based on the evaluation results, the spatial correlation analysis of changes in habitat quality was further carried out. The autocorrelation index was 0.5122, which indicating that the changes in ecological environment quality in the study area has a strong spatial aggregation characteristics. Combined with the change in land use changing in the present study, we found that the human activities were the major factor causing the changes in ecological environment quality in the study area. These results can provide certain theoretical basis and technical support for land development and utilization as well as for the ecological protection in the study area.