Dramatic environmental changes have been recently reported in the Yellow Sea (YS), the South Sea of Korea (SS), and the East/Japan Sea (EJS), but little information on the regional primary productions is currently available. Using the 13C-15N tracer method, we measured primary productions in the YS, the SS, and the EJS for the first time in 2018 to understand the current status of marine ecosystems in the three distinct seas. The mean daily primary productions during the observation period ranged from 25.8 to 607.5 mg C m−2 d−1 in the YS, 68.5 to 487.3 mg C m−2 d−1 in the SS, and 106.4 to 490.5 mg C m−2 d−1 in the EJS, respectively. In comparison with previous studies, significantly lower (t-test, p < 0.05) spring and summer productions and consequently lower annual primary productions were observed in this study. Based on PCA analysis, we found that small-sized (pico- and nano-) phytoplankton had strongly negative effects on the primary productions. Their ecological roles should be further investigated in the YS, the SS, and the EJS under warming ocean conditions within small phytoplankton-dominated ecosystems.