The ecological effect of land use change has become a core issue in ecological studies. Analyzing the spatial and temporal changes in habitat quality caused by land-use change can provide a scientific basis for ecological protection and land planning. Taking Fujian Province as an example, we utilized the InVEST model to evaluate habitat quality. The habitat in Fujian can be classified into low, medium, good, and excellent grades based on the habitat quality index. We also analyzed the influence of land-use change on the spatiotemporal characters of habitat quality in Fujian Province. The results showed that: from 2000 to 2010, the landscape fragmentation index for Fujian Province gradually decreased, the connectivity between patches was acceptable, the extent of habitant fragmentation was improved, and the overall habitat value was higher than 0.9. In Fujian Province, woodland is a beneficial landscape covering almost 86% of the lands. The degree of fragmentation was quite low with little human interference; therefore, the majority of habitats in Fujian Province were of good and excellent quality. However, the southeast coastal areas of Fujian Province are of low and poor habitat quality (less than 0.6), the reason for which might be the rapid expansion of construction land that has increased the extent of damage to habitat quality. More than 65% of the GDP in Fujian Province can be attributed to the southeast coastal areas, and the structure of secondary or tertiary industries increasing the demand for infrastructure, industry, and residential land. As a consequence, more than 57% of the construction land in Fujian Province is concentrated in the southeast coastal areas. The high density of construction land in these areas has seriously encroached on large areas of bare land and farmland, disturbed the entire ecological pattern of the area, and destroyed habitat quality, which accounts for the typically lower habitat quality in the southeast than in other areas of Fujian Province.