<p>With the development of the social economy and the frequent occurrence of extreme rainfall events, the risks of flooding are on the rise. Traditionally, flood models focus on calculating flooding risk for a single rainfall event. They are not available for the decision-making of long-term lifecycle activities (such as priority of flooding region point remediation and determination of the flooding insurance premium rate). In this study, a long-term areal flooding risk calculation method was proposed to quantify the comprehensive effects of extreme rainfall events over years. First, the division and sampling method of targeted rainfall events was proposed based on the annual maxima sampling (AMS) method, and the corresponding empirical frequency was calculated using the Weibull formula. Additionally, an algorithm for flood diffusion and inundation was developed for the target region using the binary search and isovolumetric methods, accounting for variations in catchment area based on rainfall return periods. Thus, the long-term areal flooding risk was calculated according to the formula of “Risk = Probability (the empirical frequency was used in this study) × Consequence (inundation volume and area were used in this study)”. Finally, a long-term areal flooding risk evaluation software (Risk-SWMM) was developed based on the EPA SWMM engine, and a case study was conducted based on the recorded rainfall series (from April 19, 2016, to September 30, 2024). Results showed that: (1) A new method was proposed for calculating the long-term areal flooding risk. It can support decision-making for flooding risk management in flood-prone areas. (2) The proposed method considered the variation relationship between the upstream catchment scope of the target region and the return periods of rainfall events. (3) The annual maxima sampling (AMS) method was used to sample the target rainfall events for flooding risk calculation.</p>