Quantitative analysis of benthic foraminifera from ODP Site 1146 in the northern South China Sea shows that the abundance of Bulimina alazanensis, sometimes up to about 90%, decreased gradually since 3.2 Ma, especially at 2.1 Ma. The abundance of other benthic foraminiferal species, i.e., Globobulimina subglobosa and Cibicidoides wuellerstorfi, increased after 2.1 Ma. A comparison of changes in oxygen and carbon isotopes in planktonic and benthic foraminifera shows that the high abundance of B. alazanensis corresponds with lower values of oxygen isotopes, but is consistent with heavier carbon isotopes in benthic foraminifera and lighter carbon isotopes in planktonic foraminifera, and vice versa. Considering factors such as the uplift of the Bashi Strait, the expansion of the Northern Hemisphere Glaciation, the strengthening of the East Asian winter monsoon and variations in oxygen and carbon isotopes in foraminifera, changes in B. alazanensis at ODP Site 1146 suggest that the source of deep water masses in the northern South China Sea changed from the warm Pacific deep water with a high oxygen content to the Pacific intermediate water with a low oxygen content at 2.1 Ma. In addition, the strengthened East Asian winter monsoon resulted in increased primary productivity, high nutrient levels, and suboxic bottom water. Variations in species of B. alazanensis seemed to be unable to tolerate the environmental stress induced by deep water masses and productivity changes.