Dokdo, a volcanic island located in offshore waters, is significantly influenced by various currents and the island effect resulting from upwelling events. Despite these factors, there is a limited understanding of the seasonal changes in phytoplankton populations and their relationship with the environmental factors in the waters around Dokdo, even during dramatic shifts in phytoplankton dynamics. We focused on seasonal oceanographic features over three years (2018, 2019, and 2020) to understand the phytoplankton community structure and seasonal species succession. Winter, characterized by thorough mixing, results in high nutrient levels, leading to increased phytoplankton biomass. The dominance of the large-sized diatom Chaetoceros spp. contributes to relatively low diversity (H’: 1.14 ± 0.31). In contrast to the typical coastal waters, spring exhibits dominance by the small nano-flagellates and Cryptomonas spp. associated with a lack of surface nutrients due to increased water temperature. Summer, characterized by strong stratification, shows low phytoplankton biomass but high Chl. a concentrations, possibly influenced by picoplankton and the emergence of dinoflagellates, such as Gyrodinium sp. and Katodinium sp., which increases diversity (H’: 2.18 ± 0.28). In autumn, there is typically a phytoplankton bloom, but in 2019, an unusually low biomass occurred. This was likely due to the intrusion of deep, cold water from the bottom and low-salinity Changjiang diluted water (CDW) from the surface, increasing the water’s stability. This, in turn, led to nutrient depletion, contributing to a rise in diversity (H’: 1.14 ± 0.31). These environmentally complex waters around Dokdo result in a distinct pattern of biodiversity indices, with the highest in summer and the lowest in winter, differing from typical temperate waters. In conclusion, this research highlights the substantial influence of distinctive oceanographic features and nutrient dynamics on the phytoplankton biomass and biodiversity in the Ulleung Basin and Dokdo region. Understanding these patterns is vital for the effective management of marine ecosystems and fisheries resources, emphasizing the necessity for continued long-term monitoring in the vicinity of the Dokdo area.