Despite the Yangtze River Basin (YRB)’s abundant land and forestry resources, there is still a dearth of research on forecasting habitat quality changes resulting from various geographic and environmental factors that drive landscape transformations. Hence, this study concentrates on the YRB as the focal area, with the aim of utilizing the Patch Landscape Upscaling Simulation model (PLUS) and the habitat quality model to scrutinize the spatial distribution of landscape patterns and the evolution of HQ under four scenarios: the natural development scenario (NDS), farmland protection scenario (CPS), urban development scenario (UDS), and ecological protection scenario (EPS), spanning from the past to 2030. Our results show that (1) from 2000 to 2020, the construction land in the YRB expanded at a high dynamic rate of 47.86% per year, leading to a decrease of 32,776 km2 in the cultivated land area; (2) the UDS had the most significant expansion of construction land, followed by the NDS, CPS, and EPS, which had higher proportions of ecologically used land such as forests and grasslands; (3) from 2000 to 2020, the HQ index ranged from 0.211 to 0.215 (low level), showing a slight upward trend, with the most drastic changes occurring in the low-level areas (−0.49%); (4) the EPS had the highest HQ (0.231), followed by the CPS (0.215), with the CPS increasing the HQ proportion of the lower-level areas by 2.64%; (5) and in addition to government policies, NDVI, DEM, GDP, and population were also significant factors affecting landscape pattern and changes in habitat quality.