Regional habitat quality is a proxy of biodiversity. Simulating changes in land use and habitat quality in urban agglomerations is the scientific basis for promoting the optimal allocation of land resources and building ecological civilizations in urban agglomerations. Therefore, we established a research framework mainly consisting of the Future Land Use Simulation (FLUS) model with the Integrated Valuation of Environmental Services and Tradeoffs (InVEST) model to predict the spatial and temporal distribution of habitat quality. In addition, we set three scenarios which were a natural development scenario, a cultivated land protection scenario, and an ecological protection scenario to analyze the changes of habitat quality in the Guanzhong Plain urban agglomeration in 2035. The results showed that: (1) the FLUS model had an excellent effect on the simulation of land-use change in the Guanzhong Plain urban agglomeration, with an overall accuracy of 0.952 and a kappa coefficient of 0.924. (2) From 2000 to 2035, the cultivated land area of the study area, which was mainly transferred into construction land and grassland, shrank due to the process of urbanization. (3) The habitat quality score of this region gradually decreased from 2000 to 2020, and it continued to decrease to 0.6921 in 2035 under the natural development scenario, while it increased under the other two scenarios. The low-value areas of habitat quality were mainly located in the middle of this region with Xi’an as the core, whereas the high-value areas were mainly distributed in the southern Qinling Mountains and the northern Loess Plateau. (4) Of the different scenarios, the ecological protection scenario had the highest habitat quality, while the natural development scenario had the lowest. Besides this, we also found that the cultivated protection scenario had high habitat quality, which was mainly because the rate of occupation of ecological land was controlled. The results are expected to provide a scientific basis for optimizing the spatial allocation of land resources and promoting the sustainable use of land space in other ecologically fragile urban agglomerations.