Based on the concentration and distribution pattern analysis of the rare earth elements (REEs) at the Shell Bar section from Qaidam Basin, we studied the geochemical fractionations of REE in paleolake deposits and their paleo-environmental significance. Our results show that the REE concentration in AS (acid soluble) and AR (acid residual) fractions are 20.9 μg/g and 95.4 μg/g (except element Y) individually, showing a strong REE differentiation between AS and AR fractions. However, the two types of fractions (AS & AR) have similar REE distribution patterns, which are slightly rich in light earth rare elements (LREEs), with slightly right-tilting and negative Eu anomaly. The LREE of AR is richer than that of AS. There were no significant correlations between the REE in AS, AR and other proxies. It indicated that the lacustrine deposition had different material sources and experienced varying geochemical procedures. Correlation analysis between the REE and the content of fine grain-size (<4 μm) of the sediments, Rb/Sr ratio and Mn concentration showed high correlation coefficients. Our results demonstrated that the REE in acid soluble and residual fractions bear different environmental significances, which are strongly dependent on local environment. The REE of acid soluble fraction is closely related to the paleoclimatic changes in the lake catchment and the evolutionary processes of lake itself. Our results suggest that δCe and (La/Yb)n could be used as proxies of the reduction-oxidation conditions and furthermore the temperature change and the lake level fluctuations. Using these proxies, we reconstructed the paleoclimate and water level fluctuation history during the high lake level period lasting between 43.5 and 22.4 cal. ka BP.