Altay region is located in the northern part of Xinjiang, and has complex and diverse internal geomorphic types, undulating terrain and a fragile ecosystem. Studying the impact of land use changes on habitat quality is of great significance to regional ecological protection and development, rational planning and utilization, and ensuring the sustainable development of the ecological environment. Based on the InVEST model, combined with land use panel data and topographic relief data of the Altay region, this paper studied the habitat quality from 1995 to 2018. The results show that cultivated land, water area and construction land increased gradually from 1995 to 2018, while grassland and unused land decreased. Forestland remained stable in the first five periods, but increased significantly in 2018. During 1995–2018, all land use types were transferred, mainly between cultivated land, forestland, grassland and unused land in the flat and slightly undulating areas. Poor habitat quality was dominant during 1995-2018. Habitat quality decreased significantly in 2015, which was related to the rapid expansion of cultivated and construction land as threat sources, as well as the decrease of forest and grassland as sensitive factors. However, habitat quality improved significantly in 2018, because a large amount of cultivated land and unused land were converted into forest land and grassland with high habitat suitability. Land use type has an important influence on habitat quality. The distribution characteristics of habitat quality for topographic relief types from good to bad were: large undulating area>medium undulating area>small undulating area>flat area>slightly undulating area. The findings of this study are of great significance for coordinating social, economic, and ecological development in this region and in similar areas.