As the third largest watershed in China, the Pearl River Basin is characterized by a dense population, an intricate network of waterways, and a high concentration of economic activities. Accelerated urbanization and the promotion of intensive agriculture within this region have led to increased inputs and losses of exogenous carbon (C), nitrogen (N), and phosphorus (P), posing severe challenges to water environmental safety and ecosystem balance in the Pearl River Delta and estuarine areas. Against the backdrop of global climate change and the "Dual Carbon" strategy, understanding the mechanisms of synergistic migration, retention, and transformation of C, N, and P elements driven by the water cycle at the basin scale holds significant scientific meaning and practical application value for water resource protection and pollution control. This study is based on the eco-hydrological coupling model HEIFLOW. It integrates multi-source data such as meteorological, hydrological and socio-economic data to construct a simulation model for the carbon-nitrogen-phosphorus coupled cycle in the Pearl River Basin. It analyzes the carbon balance and source-sink patterns of the basin, conducts scenario simulations to quantify the contributions of different human activities, and predicts future changes. The research aims to provide a scientific basis for the precise management of the water environment in the Pearl River Basin.