Abstract: Seagrass beds play a vital role as coastal blue carbon ecosystems, offering a range of ecological benefits such as habitat provision, sediment stabilization, water quality regulation, and carbon sequestration. One of the key players in such ecosystems is Zostera japonica, a dominant seagrass species found in the intertidal zone of the Yellow River Estuary. However, accurately tracking its seasonal distribution remains challenging since factors like tidal inundation, water turbidity, backgrounds of exposed tidal flats, and seasonal canopy changes all strongly affect its spectral response. This study zoomed in on the intertidal Zostera japonica seagrass beds across the Yellow River Estuary, blending multi-source Sentinel and Landsat imagery from 2023 to 2025. A seasonal SeaGrass Index (SGI) was developed, and the Multi-Otsu thresholding method was employed to delineate areas with a high likelihood of seagrass presence. We then ran area statistics, analyzed spatial overlays, and used seasonal combination coding to map out the seasonal distributions and spatial organization. According to our findings, the high-probability distribution area of Zostera japonica varied distinctly with the seasons. The largest distribution was observed in summer, during the species′ rapid growth phase, reaching 382.48 hm². In comparison, the distribution areas for spring, autumn, and winter were 231.73 hm², 46.10 hm², and 92.22 hm², respectively. Spatial comparison across seasons revealed that spring and summer exhibited the strongest spatial continuity, whereas the overlap between summer and autumn and between autumn and winter diminished markedly. The coding for seasonal combinations further highlighted considerable spatial heterogeneity. Approximately 40.11% of the four-season union area was shared by spring and summber while the summer-only area spanned 151.90 hm², making up 31.25% of the union area. In stark contrast, the consistently identified area across all four seasons covered just 0.04% of the union area. These patterns suggest that the seasonal distribution of Zostera japonica meadows is not centered around a large, persistent year-round core. Instead, it is a mosaic of areas that recur over multiple seasons, areas that expand in summer, as well as single-season fluctuating areas. Field observations conducted during summer and early autumn generally supported the remotely sensed identification of the main seagrass patches. However, there were some sparse, low-cover shoots outside the high-probability zones, which implied potential omission by medium-resolution imagery. Since the signals from winter canopies were weak, the winter high-value areas were interpreted conservatively as potential seagrass-like spectral candidates rather than confirmed seagrass coverage. Overall, the seasonal spatial organization uncovered in this study enhances remote sensing analysis of seagrass, moving beyond simple distribution mapping to a deeper understanding of seasonal spatial patterns. Our results lay a valuable foundation for grasping seasonal variability in intertidal Zostera japonica meadows and may aid in seasonal monitoring, conservation zoning, and restoration management along the Yellow River Estuary.