Accurate extraction of Seasonally Inundated Area (SIA) is pivotal for precise delineation of Flood Inundation Area (FIA). Current methods predominantly rely on Water Inundation Frequency (WIF) to extract SIA, which, due to the lack of analysis of dynamic surface water changes, often yields less accurate and robust results. This significantly hampers the rapid and precise mapping of FIA. In the study, based on the Harmonic Models constructed from Long Time-series Surface Water (LTSW) dynamics, an SIA extraction approach (SHM) was introduced to enhance their accuracy and robustness, thereby improving flood mapping. The experiments were conducted in Poyang Lake, a region characterized by active hydrological phenomena. Sentinel-1/2 remote sensing data were utilized to extract LTSW. Harmonic analysis was applied to the LTSW dataset, using the amplitude terms in the harmonic model to characterise the frequency of variation between land and water for the surface units, thus extracting the SIAs. The results reveal that the harmonic model parameters are capable of portraying SIA. In comparison to the commonly used WIF thresholding method for SIA extraction, the SHM approach demonstrates superior accuracy and robustness. Leveraging the SIA extracted through SHM, a higher level of accuracy in FIA extraction is achieved. Overall, the SHM offers notable advantages, including high accuracy, automation, and robustness. It offers reliable reference water extents for flood mapping, especially in areas with active and complex hydrological dynamics. SHM can play a crucial role in emergency response to flood disasters, providing essential technical support for natural disaster management and related departments.