A great number of calcareous nannofossils have been found in the 2.32 Ma deep-sea sediments of ODP Site 1143 located in the Nansha area, southern South China Sea. The number of coccoliths varies from about 0.5X10 (super 6) up to almost 53X10 (super 6) coccoliths/g sediment, with an average of 16X10 (super 6) coccoliths/g sediment. The accumulation rate of total coccoliths varies from 1X10 (super 6) to 278X10 (super 6) coccoliths/cm (super 2) ka. The nannofossil assemblages are usually dominated by a lower-photic species Florisphaera profunda, of which the average percentage is about 70% in all samples. The absolute abundance and the accumulation rate of nannofossils as well as the percentage of F. profunda display significant oscillations on two different time scales. One is the fluctuation coincident with the glacial-interglacial cycle, and the other is long-term changes on a time scale longer than 100 ka. Six evolutionary stages of calcareous nannofossils could be divided for the last 2.32 Ma, from which we can reconstruct the changes in the depth of the nutricline in the Nansha area. In this paper, the possible mechanism that resulted in these variations is also discussed.