Habitat quality plays a crucial role in enhancing the regional ecological environment and safeguarding biodiversity, with topography being a key element influencing the structure and function of ecosystem services. This research aims to assess habitat suitability across various topographic gradients, analyze the spatial heterogeneity of habitat quality between 2000 and 2020, and explore the relationship between influencing factors and habitat quality. InVEST model is used to evaluate the spatial-temporal evolution characteristics of habitat quality in Zhaotong City, focusing on how topographic gradients impact habitat quality distribution. The study also delves into the factors affecting habitat quality in Zhaotong City, including land use patterns, elevation, slope, average annual temperature and other variables. The results indicate three key aspects of this system. (1) During the study period, the land use types were mainly forest land, farmland and grassland, with construction land experiencing the most significant increase. (2) From 2000 to 2020, the quality areas of high and medium habitats in Zhaotong City decreased, while the quality areas of medium-high, medium-low and low habitats increased. (3) The study revealed a notable topographic gradient effect on habitat quality, with the primary driver shifting from GDP to land use type and subsequently to average annual precipitation in Zhaotong City. The transfer between different grades of habitat quality mainly presents the characteristics of “descending” transfer, with medium-low quality habitats typically found on medium-low topographic gradients and medium-high quality habitats on medium-high gradients. Cross-detection results show that land use type exhibited the strongest correlation with other influencing factors. Therefore, this study can provide a scientific basis for policy makers to protect biodiversity, enhance ecosystem services and promote regional economic development.