Upper water structure over the last 4 million years in the northern South China Sea (SCS) was reconstructed by sea surface temperature (SST) and primary productivity estimated by changes in the abundance of planktonic foraminifer, planktonic foraminifer transfer function, and the accumulation rate of benthic foraminifera. Results of SST and primary productivity show that 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. Comparison with tectonics and orbital variations indicates that phased rising of the Tibet since 3.6 Ma, closing of Panama and Indonesian seaways, and orbital changes were responsible for the changes of upper water structure in the SCS, respectively.