The redox state of ancient seawater is crucial to understanding the variations in atmospheric and oceanic conditions in the geological past. Rare earth elements + Y (REY) in marine carbonates are believed to be one potential proxy for rebuilding paleoredox conditions. The impact of diagenetic alterations on REY distribution patterns and the Cerium anomaly, however, remains debatable. One deep well (NK1) was recently drilled on an isolated coral atoll in southern South China Sea (SCS). Because it is far away from land, carbonates from Well NK1 contain very low terrigenous concentrations. Quaternary carbonates from Well NK1 with minimal terrigenous contamination are used to systematically investigate the sole effect of diagenesis on the REY geochemistry. Different diagenetic realms, including meteoric diagenesis and dolomitization, are present in Quaternary carbonates on Meiji Atoll according to petrographic observations, X-ray diffraction analyses, and δ¹³C and δ¹⁸O results. Analyses on REY compositions in different diagenetic carbonates from Well NK1 show that the seawater-like REY patterns appear not to vary with the changes in diagenetic facies. And the Ce anomaly appears to have no correlations with isotopic, elemental and mineralogical proxies for carbonate diagenesis. This study confirms the conservative behavior of REY in reefal carbonates during various diagenetic transformations in the condition of low terrigenous contaminations. This study further supports the use of REY compositions of reefal carbonates to study the seawater compositional change in the past.