Watershed habitat quality is the material basis and environmental guarantee for biological survival and sustainable development, and land use change is the most important threat factor for habitat quality. Therefore, analyzing the temporal-spatial evolution characteristics of land use and regional habitat quality is of great significance to regional biodiversity conservation and sustainable land use. In this study, took Min River Basin as the research area, based on the spatial data of land use from 2000 to 2015, a CA-Markov model was constructed to simulate the spatial data of land use under the existing development and ecological protection scenarios from 2025 to 2040, and the InVEST model was used to analyze the spatial pattern of habitat quality from 2000 to 2040. The results show that:(1) The forest coverage rate of Min River Basin is relatively high under the current conditions, the area of paddy field, dry farm, theropencedrymion, shrubwood, grassland and wetland showed a downward trend, of which grassland presented the largest decrease with the rate, of 44.64%. The coniferous forest, broad-leaved forest, water area, construction land, traffic land, mining land, and bare land were on the rise. Among them, transportation land presented the largest increase, 227.27%. The simulated land use Kappa coefficient was 89.09%, showed that the simulation result was good, and the designed ecological protection scenario was outstanding at the future land use pattern optimization. (2) During the study period, the Min River Basin generally showed high habitat quality and it basically maintained at the level of 0.82. The construction land area was the main distribution area with low habitat quality in the study area, and the downstream Fuzhou and Changle had the gathering area of largest low-value habitat quality. The distribution of habitat quality had a certain correlation with topographical conditions, and the low-value areas were mostly areas with lower altitudes. (3) From 2000 to 2015, the habitat quality of Min River Basin generally showed a declining trend, and the rate of decline increased gradually, up to 0.24%. The declining trend of habitat quality under natural development scenarios was not effectively alleviated. It was obtained under ecological protection scenarios, and the proportion of grids with the highest quality habitats was the largest with the highest proportion of 87.42%. (4) Habitat levels in the upper and middle reaches of Min River Basin were higher than those in the lower reaches. Under natural development scenarios, the gap of regional habitat quality would show an expanding trend. In the ecological protection scenario, each region would basically maintain the habitat quality level in 2015. The research results of this article can provide scientific basis and decision-making reference for sustainable utilization of land resources and biodiversity protection in Min River Basin, and promote regional sustainable development.