The Pacific Deep Water (PDW) intrudes the South China Sea (SCS) through the Luzon Strait, forming the robust overflow. It acts as an engine of the SCS deep circulation, which as an important part of global thermohaline circulation plays an important role in modulating global climate. However, the forming time and evolving process of the deep SCS overflow remains unclear. Moreover, how the East Asian Monsoon (EAM) affects the SCS deep water is not clear. Here we present two 6-Myr fossil fish teeth neodymium isotopic (eNd) records from the SCS. One is from Ocean Drilling Program (ODP) Site 1148 (18°50.169’N, 116°33.939’E, water depth 3294 m) in the northern SCS and the other is from ODP Site 1143 (9°21.72’N, 113°17.11’E, water depth 2772 m) in the southern SCS. The eNd of the fish teeth is a reliable quasi-conservative ocean circulation tracer. Modern observation demonstrates that the seawater eNd of the SCS is a mixture of the eNd of the oceanic and continental end members, namely the intruded West Pacific water masses and the sediment supplied to the SCS from the surrounding continents. The eNd records of the continental end member show constant changes over the past 6 Myr, but that of the oceanic end member is more variable. The fish teeth eNd at ODP Sites 1148 and 1143 change between -4 and -7, apparently in between the continental and oceanic end members. The eNd record of the fish teeth at ODP Site 1143 in the southern SCS is quite stable over the past 6 Myr, within a narrow range of -6 to -7. Between ~4.88 Ma and ~4.12 Ma, however, a significantly rapid increase as much as 2.6 (from -6.82 to -4.22) is seen in the eNd record of the fish teeth at ODP Site 1148 in the northern SCS, and a remarkably secular decrease as much as 3.27 (from -3.52 to -6.79) after that is observed between ~3.02 Ma and 1.314 Ma. The relatively constant eNd of the fish teeth at ODP Site 1143 indicates continuously prevailing influences of the surrounding rocks on seawater eNd in the southern SCS over the past 6 Myr. Whereas, the more positive and variable eNd at ODP Site 1148 in 4.88-1.314 Ma indicates dominated influences of PDW on seawater eNd in the northern SCS during this period. At ODP Site 1148, the steep increase in the fish teeth eNd from 4.88 Ma to 4.12 Ma indicates abruptly strengthened deep SCS overflow, whereas the gradual decrease from 3.02 Ma to 1.314 Ma suggests gradually intensified East Asian summer monsoon during this period.