Check dams are applied worldwide as an effective approach for soil and water conservation. To improve the simulation accuracy of the hydrological processes in a catchment with a check-dam system, this study analyzed the applicability and accuracy of a formula for the drainage process of a perforated riser principal spillway based on observational experiments. The rainfall-runoff processes in a catchment with a check-dam system were also simulated with the recommended formulas for the drainage process of a perforated riser principal spillway. The deviations in the calculated discharge from the observed values of the experiment with the recommended formulas under normal and abnormal working conditions were within ±15% and ±5%, respectively. The hydrologic model used in this study needed only a few parameters to achieve a satisfactory simulation accuracy. The recommended formulas for the drainage process of a perforated riser principal spillway can improve the simulation accuracy of a flood peak by 7.42% and 19.58% compared with the accuracies of the technical code formula scenario and no drainage scenario, respectively. The results of this study are expected to provide a reference for flood warnings and safe operations of check-dam systems.