In ecologically fragile areas, an uncontrolled increase in urban development intensity (UDI) will erode the ecological carrying capacity (ECC). This study aimed to explore the relationship between UDI and ECC and quantify the impacts of UDI on ECC. The Three Gorges Reservoir Area (Chongqing section) was chosen for the case study. Firstly, the UDI and ECC were comprehensively evaluated. Then, the coupling coordination relationship between the two was analyzed by a coupling coordination degree model. Finally, the influences of UDI on the coordinated development of the two were analyzed by a geographically weighted regression model. The results show that the distributions of UDI and ECC are opposite; UDI and ECC are mutually restricted to some extent. UDI and ECC are moderately coupled and poorly coordinated, and a higher UDI is mostly correlated to a higher coordination degree of UDI and ECC. In areas with higher UDI, an appropriate control on population and economy may benefit the coordinated development. Meanwhile, in areas with lower UDI, the promotion of population aggregation and economic investment would enhance the coordinated development between UDI and ECC. This study could optimize the dimensional control of UDI, which contributes to the long-term sustainability of ecologically fragile areas.