Timing of sea ice retreat (TSR) as well as cell size of primary producers (i.e., phytoplankton) plays crucial roles in seasonally ice-covered marine ecosystem. Thus, it is important to monitor the temporal and spatial distribution of phytoplankton community size structure. Prior to this study, an ocean color algorithm has been developed to derive phytoplankton size index F L , which is defined as the ratio of chlorophyll a derived from the cells larger than 5 μm to the total chl a using satellite remote sensing for the Chukchi and Bering shelves. Using this method, we analyzed pixel-by-pixel relationships between F L during marginal ice zone (MIZ) bloom period and TSR over a period of 1998–2013. The influence of TSR on sea surface temperature (SST) and changes in ocean heat content (ΔOHC) during the MIZ bloom period were also investigated. A significant negative relationship between F L and TSR was widely found in the shelf region during MIZ bloom season. On the other hand, we found a significant positive (negative) relationship between SST (ΔOHC) and TSR. That is, earlier sea-ice retreat was associated with a dominance of larger phytoplankton during a colder and weakly stratified MIZ bloom season, suggesting that duration of nitrate supply, which is important for large-sized phytoplankton growth in this region (i.e., diatoms), can change according to TSR. In addition, under-ice phytoplankton blooms are likely to occur in years with late ice retreat, because sufficient light for phytoplankton growth can pass through the ice and penetrate into the water columns due to an increase in solar radiation toward the summer solstice. Moreover, we found not only the length of ice-free season but also annual median of F L positively correlated with annual net primary production (APP). Thus, both phytoplankton community composition and growing season are important for APP in the study area. Our findings showed quantitative relationship between the inter-annual variability of F L , TSR and APP suggesting satellite remote sensing of phytoplankton community size structure is suitable to document the impact of recent rapid sea ice loss on ecosystem of the study region.