By considering the supply state of ecosystem service, the ecosystem pressure of urbanization and the restoration potential of economic development in territorially ecological restoration zoning, it can help to provide a spatial approach for the integration of naturally ecological system and socioeconomic system, and to promote the overall protection and coordinated governance of regional ecosystem. Based on the framework of degradation pressure, supply state and restoration potential, this study fully assessed the pressure, state and potential of the ecosystem to identify the territorially ecological restoration zoning in the Pearl River Delta. The results showed that the pressure index formed a series of high-value areas in the core area of Pearl River Delta and gradually radiated to the central cities of Zhaoqing City, Huizhou City and Jiangmen City. The spatial distribution of supply index was different, for which there is no natural transition between low and high values. The high-potential index areas were mainly located in highly developed urban centers. The territorially ecological restoration zoning in Pearl River Delta were divided into five categories. Among them, the ecological priority restoration zone (high pressure, low supply and low potential) was located in the border area of Guangzhou-Foshan metropolitan area, Dongguan City, and the central city of Zhongshan City and Zhuhai City, accounting for 9.39% of Pearl River Delta, which was in urgent need of special funds for territorially ecological restoration to carry out inter-regional coordinated governance. The ecological control zone (low pressure, low supply and low potential) was mainly located in Nansha District of Guangzhou City, and the non-central city of Foshan City, Zhongshan City and Zhuhai City, accounting for 12.98% of Pearl River Delta. It was necessary to promote regional economic development within the scope of resource and environment. The ecologically autonomous restoration zone (high pressure, low supply and high potential) was mainly located in Baoan District, Nanshan District and Futian District of Shenzhen City, the central city of Guangzhou City and Chancheng District of Foshan City, accounting for 3.24% of Pearl River Delta. The region should adhere to the implementation of regionally ecological restoration policies and investment in environmental governance. The results clarified the territorially ecological restoration zoning in the Pearl River Delta region, which would provide decision guidance for the system layout of ecological restoration projects.