The SCS curve number (SCS-CN) method has gained widespread popularity for simulating rainfall excess in various rainfall events due to its simplicity and practicality. However, it possesses inherent structural issues that limit its performance in accurately simulating rainfall excess and infiltration over time. The objective of this study was to develop a modified CN method with temporally varying rainfall intensity (MCN-TVR) by combining a soil moisture accounting (SMA) based SCS-CN method with the SMA method in the Hydrologic Engineering Center’s Hydrologic Modeling System (HEC-HMS). In the MCN-TVR, the SMA-based SCS-CN method is utilized to simulate the cumulative rainfall excess and infiltration, while the SMA method in the HEC-HMS serves as an infiltration control function. A key advantage of the MCN-TVR is that it eliminates the need for additional input parameters by inherently linking the parameters in the two SMA-based methods. Sixteen hypothetical 24 h SCS Type II rainfall events with different soil types and five real rainfall events for the Rush River Watershed in North Dakota were used to assess the performances of the MCN-TVR method and the SMA-based SCS-CN method. In the hypothetical simulations, the rainfall excess simulated by the SMA-based SCS-CN and MCN-TVR models was compared to that simulated by a Green–Ampt model. Discrepancies were observed between the rainfall excess simulated by the SMA-based SCS-CN and Green–Ampt models, especially for coarse soils under relatively light rainfall. However, the MCN-TVR model, incorporating an infiltration control function, demonstrated its improved performance closer to the Green–Ampt model. For all the hypothetical events, the Nash–Sutcliffe efficiency (NSE) coefficient of the rainfall excess simulated by the MCN-TVR method compared to the Green–Ampt model was greater than 0.99, while the root mean standard deviation ratio (RSR) was less than 0.03. In the real applications, the SMA-based SCS-CN model failed to provide acceptable simulation of the direct runoff for rainfall events with durations of less than the time of concentration. In contrast, the MCN-TVR model successfully simulated the direct runoff for all the events with NSE values ranging from 0.65 to 0.91 and RSR values from 0.31 to 0.56.