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Phytoplankton are indispensable part of the marine ecological environment, and their size class (PSC) is a key parameter to describe the vital role of phytoplankton in different geobiochemical cycles. The Yellow Sea, the Bohai Sea and the East China Sea are located in the eastern part of China as a whole, shown as semi-closed characteristics. The PSC field measurement is mainly dependent on the in situ cruise observation experiments carried out in recent years. The sampling points are sparse and uneven in space and time. Therefore, it is necessary to use high Remote sensing inversion technology with a wide range of frequency and coverage to fill the insufficiency of field measured data. Based on the sea surface remote sensing reflectance products of MODIS/Aqua sensors from 2002-08 to 2021-07, this paper applies the PSC remote sensing inversion model constructed by Sun et al. (2019) to produce PSC long-term data set. The data set is stored in the standard format of Matlab and contains 228 files in total, which are easy to read by each software (DOI: 10.17632/mjg5s9p4wp.3). The product accuracy verification results show that the satellite inversion and the field measurement results are relatively consistent (the average absolute percentage error is 22.9%, 11.4%, and 35.0% for micro, nano, and picophytoplankton, respectively). At the same time, the comparison of spatial distribution in different sea areas shows that the PSC inversion after reconstructing the chlorophyll a concentration is closer to the field measured value. The statistical results of the long-term distribution of PSCs based on this dataset show that the coastal waters are mainly enriched by microphytoplankton, while the offshore waters are primarily dominated by nanophytoplankton. Judging from the multi-year monthly averaged PSCs in five specific areas, taking microphytoplankton as an example, there are "double peaks" in spring (May) and summer (July) in the center of the Bohai Sea and the mouth of the Yangtze River, while the North Yellow Sea area presents a spring (April), autumn (October) peak feature. Meanwhile, the spring peaks in the offshore waters of the South Yellow Sea and the East China Sea are more significant in April and March, respectively. This dataset is helpful for fine-grained analysis and understanding of the temporal and spatial variation of phytoplankton in the Yellow Sea, the Bohai Sea, and the East China Sea. It can also be used as a routine project for water environment monitoring and is worthy of popularization.