Reasonable evaluation of water resources carrying capacity is an effective way to promote regional sustainable development. This paper took the Pearl River Delta city cluster as the research object, established an evaluation model based on the entropy weight of the water resources carrying subsystem, and analyzed the difference of the water resources carrying subsystem in the Pearl River Delta by combining with the grey relational theory. The results showed that there are differences between the water resources carrying subsystem and the total grade in different regions. Except for Jiangmen, Huizhou and Zhaoqing cities, the development and utilization of water resources in other areas has reached saturation point. The supply of water resources in Shenzhen, Foshan and Zhuhai is insufficient to support social and economic development and cannot meet the needs of economic development. Although the total carrying capacity of water resources is high in Jiangmen and Zhaoqing, the water efficiency is low in industry, agriculture, and daliy consumption. The high water consumption rate means that water resources are not fully utilized. The S4 subsystem in Dongguan is lower than other cities, and should be paid more attention to. The method based on subsystem entropy weight proposed in this paper can improve the current situation of traditional entropy weight distribution and provide targeted evaluation conclusions. It has important reference value for the rational allocation of governance measures of each subsystem to ensure the sustainable and coordinated development in the future.