Phytoplankton cell size is a useful ecological indicator for evaluating the response of phytoplankton community structure to environmental changes. Ocean-color remote observations and algorithms have allowed us to estimate phytoplankton size classes (PSCs) at decadal scale, helping us to understand their trends under ocean warming. Here a large data set of pigments, derived through high performance liquid chromatography, was collected in the Bohai Sea (BS) and Yellow Sea (YS) between 2014 and 2016. The data set was used to reparametrize the sea surface temperature (SST)-dependent threecomponent model of Brewin et al. (2017) to the region. The model was validated using independent in situ data set and subsequently applied to satellite chlorophyll-a data from Ocean Colour Climate Change Initiative, spanning from 1997 to 2016, to derive percentages of three PSCs to total chlorophyll-a. Monthlyaveraged PSCs exhibited spatial-temporal variations in the study area, linked to topography, temperature, solar radiation, currents, and monsoonal winds. In the surface central south Yellow Sea (SYS), influenced by bottom Yellow Sea Cold Water Mass, tight relationships between PSCs and environmental factors were observed, where high SST, high sea level anomaly, low mixed-layer depth, and low wind speed resulted in higher proportions of nanoplankton and picoplankton from June to October. Significant interannual anomlies in PSCs were found associated with El Niño events in the central SYS, related to anomalies in SST. The refined model characterized 20-year variations in chlorophyll-a concentration and PSCs in complicated optical, hydrodynamic, and biogeochemical environments in the BS and YS.Plain Language Summary Phytoplankton are the fundamental component of the marine ecosystem, and the size structure of phytoplankton influences many processes in phytoplankton biology, marine ecology, and marine biogeochemistry. Phytoplankton can be divided into three phytoplankton size classes (PSCs): microplankton (>20 μm), nanoplankton (2-20 μm), and picoplankton (<2 μm). The Bohai Sea (BS) and Yellow Sea (YS) are shallow marginal seas in the northwest Pacific Ocean, strongly impacted by large river plumes, ocean processes, and seasonal monsoons, supporting high primary and fishery productivity. Using a 20-year time series satellite ocean color data from 1997 to 2016, and a SSTdependent model that links chlorophyll-a concentration to the size structure of phytoplankton, we observe spatial and temporal variations of PSCs in the BS and YS and tight correlations between the size structure and physical variables in the central south Yellow Sea. Interannual variations in the PSCs are coupled with changes of sea surface temperature in El Niño events. Our results demonstrate that variations in the phytoplankton size structure are coupled with changes in climate variability, with implications for how the regional ecosystem may change with predicted changes in climate.