In the context of promoting high-quality development of mountainous urban areas, it is of great significance to explore the evolutionary trajectory of habitat quality in the future based on policy-driven backgrounds, particularly for the protection of the Western mountainous ecosystem. This study takes the Chongqing metropolitan area, a typical southwestern mountainous city, as the study area. Based on land use data from 1990 to 2020, the study combines the InVEST and PLUS models, considering the constraints imposed by urban construction planning and ecological control policies, to investigate the spatiotemporal variations of habitat quality from 1990 to 2030. The findings are as follows: (1) From 1990 to 2020, there was a significant decrease in cultivated land area in the study area, while forestland and unused land showed a declining trend. Conversely, built-up land, grassland, and water bodies exhibited an increasing trend. In the land use simulation for 2030, under the scenarios of natural growth and ecological protection, the cultivated land area further decreased, while forestland and grassland received a certain degree of protection. In the scenario of development, a large amount of cultivated land was converted into built-up land. (2) From 1990 to 2030, significant overall habitat quality changes were observed among different regions within the study area. Except for Nanchuan District and Qijiang District, other administrative regions experienced a certain degree of decline in habitat quality. The distribution of habitat quality exhibited significant spatial heterogeneity. The low-value habitat areas were centered in the middle of the metropolitan area and gradually expanded outward. The high-value habitat areas were concentrated in the study area, including the Huaying Mountain range and other mountainous ecological corridor regions. (3) Habitat quality in the study area showed a decreasing trend with an increasing slope gradient. With the development of urbanization, habitat quality degradation gradually spread to high-altitude and steep-slope areas. (4) The expansion of built-up land is the main cause of habitat degradation in the study area. From 1990 to 2030, against the background of development strategies in the study area, the expansion of built-up land encroached upon cultivated land and forestland. In the habitat quality prediction for 2030, habitat degradation in the region will continue to intensify. This study provides scientific references and the basis for promoting regional sustainable land use and ecological conservation.