Since the implementation of the Chinese economic reforms, economic development in the coastal cities has resulted in serious degradation of habitat quality; however, the concept of "ecological civilization" has improved this situation. For quantitative analysis of the correlation between the Pearl River Delta urban expansion and changes in habitat quality under the influence of the policy, we first analyzed the habitat quality change based on the InVEST model and then measured the impact of construction land expansion on the habitat quality through habitat quality change index (HQCI) and contribution index (CI) indicators. Finally, the correlation between urbanization level and habitat quality was evaluated using geographically weighted regression (GWR) and the Self-organizing feature mapping neural network (SOFM). The results indicated that: (1) during the study period, the habitat quality index decreased from 0.7181 to 0.6672 owing to urban expansion, and the decrease was most significant from 2000 to 2010. (2) The urbanization index had a negative effect on the habitat quality, but this improved after 2000, reflecting the positive effect of policies such as "ecological civilization construction" (3) The importance of ecological civilization varies greatly among cities in the study area: Shenzhen, Dongguan, Foshan, and Zhongshan have the best level of green development. These results reflect the positive role of policies in the prevention of damage to habitat quality caused by economic development and provide a reference for the formulation of sustainable urban development policies with spatial differences.