As the economic center of western China, the Chengdu Chongqing Economic Zone holds a unique and important strategic position for China’s overall development. However, rapid economic growth in the region in recent years has led to an increase in the number of urban areas that threaten the preservation of local ecosystems. Therefore, it is crucial that long-term analyses and projections of habitat quality conditions in the region are conducted to ensure sustainable development, and the habitat quality index provides a valuable measure of the ecosystem health of a region. In this study, we utilized land use/land cover data of 2000–2020 to predict land use cover in the study area in 2040. A natural development scenario, a cultivated land security scenario, and an ecological priority development scenario were simulated, and the results were subsequently explored. Future land use projections were based on the artificial neural network-cellular automata model, and habitat quality details were calculated using the Integrated Valuation of Ecosystem Services and Trade-offs (InVEST) model. These methods allowed for an evaluation of the evolution of the Chengdu Chongqing Economic Zone over the past 20 years as well as predictions about the course of its development and habitat quality over the next 20 years. The results revealed the following: (1) The Chengdu Chongqing Economic Zone is mainly composed of cultivated land and forest land, followed by urban land and grassland. Between 2000 and 2020, there was a significant increase in the number of urban areas and a continuous decrease in cultivated land. On the basis of simulations and analyses of different scenarios, urban land areas are projected to increase between now and 2040. (2) In 2000, 2010, and 2020, the average habitat quality indices of the Chengdu Chongqing Economic Zone were 0.6494, 0.6432, and 0.6336, respectively, indicating good habitat quality, but one that is in decline, particularly in the urban areas of Chengdu and Chongqing. Spatial analysis revealed a pattern in which the habitat quality may be described as “high at the periphery, low in the center.” Our findings showed that over the next 20 years, the best potential for a high-quality regional habitat depends on a scenario in which ecological protection is emphasized. In 2000, 2010, and 2020, the average habitat degradation indices were 0.0935, 0.0938, and 0.0949, respectively, indicating an increasing threat to the region’s habitat. This conclusion will be beneficial to the future urban spatial planning of the area: the government should prevent the disorderly expansion of cities and maintain the biodiversity of the Chengdu Chongqing Economic Zone. The analyses and evaluation methods used in this study can also serve as a valuable reference for other regions seeking to improve their habitat quality and land use.