In this paper, core samples from the Well LS33 in the deep-water area of the Qiongdongnan Basin (QDNB) in the South China Sea were selected and analyzed by group (authigenic carbonate and terrigenous detritus) to obtain the contents of rare earth elements (REE) to explore the degree of preservation of paleo-seawater information by carbonate components and elucidate the provenance relationship between the QDNB and the Yinggehai Basin and the provenance changes in the deep-water area of the QDNB since the Oligocene. The main achievements of this paper are as follows: (1) In the process of extracting the autogenic carbonate, the iron-manganese oxide envelope on the surface of the sediment particles (which can adsorb REE or its complexes in seawater) will partially dissolve into the autogenic carbonate components, thus covering the REE geochemical information of paleo-seawater carried by the autogenic carbonate. Therefore, caution should be exercised when using the geochemical characteristics of REE in the carbonate component of impure carbonate rocks to reflect the sedimentary paleoenvironment. (2) The analysis of the REE geochemical characteristics of multiple cores in the Yinggehai-QDNB shows that there is a close provenance relationship between the two Basins. The sediments in the central depression area of the Yinggehai Basin and the deep-water area in the western part of the QDNB generally contain more feldspar (Eu-rich) minerals. Since the Eocene, paleo-rivers have carried ultramafic-mafic materials originating from the western South China Sea into the sea. Affected by the transport distance and sea level changes, the content of feldspar (Eu-rich) minerals in the sediments of the QDNB from west to east gradually decreased.