In marginal seas like the South China Sea (SCS), optic remote sensing is often blocked by clouds and sun glint, leading to high missing rates in remote sensing products of chlorophyll-a. In our previous studies, we reconstructed (gap-filled) a chlorophyll-a data set, the full-coverage, 4-km daily SCSDCT product freely distributed at https://www.scidb.cn/detail?dataSetId=1387ffe83af54f0fb574d60e97b206b2. Based on this data set, various physical-biological coupling properties in the SCS were investigated, including the Madden-Julian Oscillation’s modulation on the representative subsystems, the long-term trends of chlorophyll-a, and the properties of marine bloom events of the SCS. In this talk, I will summarize these studies and will emphasize the data science aspects within them. The potential of these data-driven approaches will also be highlighted in revealing new findings about the marine ecosystem.