Changing land use and urban expansion are key drivers of global environmental change, which are inevitable consequences of economic and social development for many cities. Most land use changes have a negative impact on the natural environment, especially due to their effects on surface temperature, runoff and habitat diversity. Due to the limitation of local government funding and expenditure, it is a challenge for developing countries to create strategies for urban sustainability. This study provided a systematic assessment method for simulating and analyzing the future impacts and spatial patterns of urban growth via cellular automata and cluster analysis. We used Tainan as a study area and compared the impact of future urban spatial development during two periods: 1993–2008 and 2008–2030. The results indicate that the impact of this development on the natural environment can be divided into six clusters. With an increased distance from the city center, there were increased changes in surface temperature and a decreased amount of runoff. These results indicate the occurrence of urban expansion, with habitat diversity being greater in areas governed by policies or ordinances.