This dataset contains nifH gene copy numbers, growth rates, and grazing mortality rates of the major unicellular cyanobacterial diazotroph taxa (UCYN-A1, -A2/3/4, -B and -C), and growth rates and grazing mortality rates of total phytoplankton community (inferred by chlorophyll a) in the South China Sea and the Luzon Strait. The associated physicochemical factors including temperature, salinity, nitrate+nitrite, ammonium, phosphate, and chlorophyll a are also available in this dataset. All these data were collected during a research cruise (Cruise No. kk1801) aboard the R/V Tan Kah Kee in early February 2018.