The Yellow Sea, characterized as a high-productivity ecosystem, is considered to be significantly attributable to high nutrient supply via atmospheric deposition. We observed a significant decline in phytoplankton biomass (~30%) over the Yellow Sea during February–May 2020 (period of COVID-19 lockdown effect) compared to the same period in 2015–2019 (period of no effect of COVID-19 lockdown). Several possible factors, such as variations in irradiance, vertical mixing, and river discharges, were not major contributors. Through the analysis of transportation and the constituents of atmospheric pollutants from Northern China (main source regions) to the Yellow Sea, we suggest that the decline in phytoplankton biomass over the Yellow Sea is mainly attributed to decreased atmospheric nutrient deposition due to the COVID-19 lockdown effect, because of decreased anthropogenic emissions in Northern China. Thus, attention should be focused on the Yellow Sea ecosystem response to increasing anthropogenic activities by lifting the COVID-19 lockdown restrictions.