This study examines the rare earth elements and yttrium (REY) concentrations of twenty-five samples from the reef outcrop exposed along the Lianglitage Mountain in the Ordovician, Tarim Basin in China. The concentration analysis provides constraints on the paleoenvironment during reef deposition. Based on the detailed sedimentology and petrographic work, we divide the reef facies into four sub-facies: the base facies, reef-core facies, reef-flank facies, and sealing facies. The geochemical data (such as major and trace elements, carbon and oxygen isotopes, and REYs) are further used to study the coeval seawater characteristics as well as potential diagenesis overprints. The result indicated that the diagenesis has little effect on the REY patterns of the reefal limestones. The REY concentrations of the reefal limestones are overall low (ranging from 3.69 to 19.60 ppm, arithmetic mean=10.22 ppm, SD=5.4). The PAAS-normalized REY patterns are consistently flat compared to the typical well-oxidized, shallow marine water patterns. However, the light REE (LREE) depletions, positive La anomalies, negative Ce anomalies and positive Y anomalies, suggest that these reefal limestones are likely an indicative of contemporaneous seawater REY signals. The seawater-like Y/Ho ratios (average at 37.51) further support that REY signals in these limestones are likely a reflection of seawater with little diagenetic modifications. The low Y/Ho ratios presented only in the reef-flank facies and sealing facies are likely a suggestion of detrital contamination. Hence, this study confirms that REY patterns of the limestones at the base facies and reef-core facies can record ancient seawater information, and reefs can be used as a potential geochemical proxy for paleoenvironment studies throughout the Earth’s history.