Continental margin ecosystems in the western North Pacific Ocean are subject to strong climate forcing and anthropogenic impacts. To evaluate mechanisms controlling phytoplankton biomass and community structure variations in marginal sea‐open ocean boundary regions, brassicasterol, dinosterol, and C₃₇ alkenones were measured in suspended particles in summer and autumn from 2012 to 2013 in the northeastern East China Sea and the western Tsushima Strait. In summer, the concentrations of brassicasterol (40–1535 ng/L) and dinosterol (4.2–94 ng/L) were higher in the southwest of Cheju Island, while C₃₇ alkenones (0–30 ng/L) were higher in the south of Cheju Island. In autumn, brassicasterol (12–106 ng/L), dinosterol (2.4–21 ng/L), and C₃₇ alkenones (0.7–7.0 ng/L) were higher in the southwest of Cheju Island and the western Tsushima Strait, and higher C₃₇ alkenones also occurred in the Okinawa Trough. Correlation analysis of biomarkers and environmental conditions (temperature, salinity, and inorganic nutrient concentrations) clearly demonstrated that phytoplankton biomass and community structure variations can be well elucidated by water masses as indexed by temperature and salinity. High nutrients from the Changjiang River were the main cause of high biomass in summer, while nutrients from subsurface water were likely the key factor regulating phytoplankton biomass in open ocean water stations in autumn. This study indicates that mechanisms controlling phytoplankton biomass in marginal sea‐open ocean boundary regions should be classified by various water masses with different nutrient concentrations, instead of by geography.