Accurate rainfall-runoff modeling is crucial for disaster prevention, mitigation, and water resource management. This study aims to enhance precision and reliability in predicting runoff patterns by integrating physical-based models like HEC-HMS with data-driven models, such as LSTM. We present a novel hybrid model, Ia-LSTM, which combines the strengths of HEC-HMS and LSTM to improve hydrological modeling. By optimizing the “initial loss” (Ia) with HEC-HMS and utilizing LSTM to capture the effective rainfall-runoff relationship, the model achieves a substantial improvement in precision. Tested in the Yufuhe basin in Jinan City, Shandong province, the Ia-LSTM consistently outperforms individual HEC-HMS and LSTM models, achieving notable average Nash-Sutcliffe Efficiency (NSE) values of 0.873 and 0.829, and average R2 values of 0.916 and 0.870 for calibration and validation, respectively. The study shows the potential of integrating physical mechanisms to enhance the efficiency of data-driven rainfall-runoff modeling. The Ia-LSTM model holds promise for more accurate runoff estimation, with wide applications in flood forecasting, water resource management, and infrastructure planning.