The structure of surface water in the northern South China Sea (SCS) over the last 4 million years was reconstructed based sea surface temperature (SST) and primary productivity estimated by changes in the abundance of planktonic foraminifera, the planktonic foraminifer transfer function, and the accumulation rate of benthic foraminifera. Results of SST and primary productivity show that the SST gradually decreased since 4 Ma, but differential seasonal temperature and primary productivity increased in steps mainly at about 3.1, 2.7, 2.1, 1.6, 0.9 and 0.5 Ma. A comparison with tectonics and orbital variations indicates that phased uplift of Tibet since 3.6 Ma, the closing of the Panama and Indonesian seaways, and orbital changes were responsible for the changes in the structure of the upper water of the SCS.