The transport and transformation process of carbon, nitrogen, phosphorus and water was developed in the Regional Integrated Earth System model (RIEMS), which included the Muskingum-Cunge method for the lateral flow of the river network and the trapezoidal river section assumption. By using river network vector extraction and the confluence area treatment with time complexity, it effectively covered small and medium-sized rivers and reasonably reflected the monthly scale changes of the river network. A computing method based on river classification is proposed. Breakpoints/virtual river sections can be set on the longest path, and the efficiency of parallel computation for the convergence of large river networks can be improved through optimization. A coupling model of the terrestrial carbon-nitrogen-phosphorus cycle and the hydrological process of the river network was developed to simulate the continuous migration of nutrient elements between the land and the river network, and the impact of nutrient limitation on regional carbon sinks was evaluated.