Based on the measured remote sensing reflectance (R_rs) and phytoplankton pigment concentrations collected during seven cruises in the Bohai Sea, Yellow Sea and East China Sea from 2016 to 2018, we established the inversion models of total chlorophyll-a, chlorophyll-b, total chlorophyll-c, photoprotective carotenoid, and photosynthetic carotenoid concentrations from the geostationary ocean color imager (GOCI) R_rs products in the coastal waters of China. Furthermore, we obtained the concentration distribution of each pigment from 2014 to 2018 in the Bohai Sea, Yellow Sea and East China Sea. The research results showed that the inversion model established by the R_rs band combinations could achieve the quantitative inversion of pigment concentration, and the inversion accuracy of the established model was relatively high (R²>0.72). As can be seen from the satellite inversion results, the phytoplankton pigment concentration presented a trend of decreasing from nearshore to offshore waters, displaying a significant seasonal variation. In conclusion, the inversion model of phytoplankton pigment concentration established in this paper can provide method support for the in-depth understanding of phytoplankton population structure and spatial-temporal variation rules in the coastal waters of China.