The simulation and prediction of runoff are crucial for the sustainable development and utilization of water resources in basins. However, due to errors in model inputs, parameters, and structure, there are also errors in the simulated runoff that need to be corrected. System differential response correction achieves the correction of the dependent variable by establishing a system response function between the dependent variable and the independent variable. This study introduces the system differential response correction method into the SWAT model. By constructing response matrices for precipitation and runoff, it corrects precipitation errors by inversing runoff errors, and then corrects runoff through model calculations. Firstly, the effectiveness of the ideal model validation method is established. Then, the Jianyang basin is selected as the study area, and the SWAT model is used to simulate and correct daily runoff. Multiple evaluation indicators are used to compare and analyze the runoff processes corrected by the system differential response correction and the autoregressive model. The research results show that the system differential response can accurately extract precipitation error information and achieve the correction of runoff sequences by correcting precipitation, and the system differential response correction for runoff in the basins is more effective than the autoregressive modeling. The multi-year average NSE increased by 24% make it suitable for runoff correction in the SWAT model.