Accurately identifying the environmental significance of phytolith assemblages in lake sediments is crucial for paleoenvironmental reconstruction. However, in arid regions, the interpretation of lacustrine phytolith assemblages can be complicated by eolian transport and post-depositional processes, resulting in environmental significance unclear. In this study, 45 samples from lake surface sediments, lakeshore soils, and eolian sands, together with a 43 cm sediment core (BRY), were collected from the hinterland of the Badain Jaran Desert. A total of 59 phytolith assemblages were analyzed using cluster analysis and transfer functions to clarify their environmental significance. Results indicate that the phytolith assemblages in lake sediments are of mixed origin, derived from both lakeshore and megadune vegetation. This suggests that they reflect the hydroclimatic conditions of the lake basin, rather than serving as a direct proxy for precipitation. Moreover, phytoliths in lake sediments can be dissolved under high-pH conditions, resulting in a very low abundance of GSSCPs. Due to the influence of lakeshore moisture and selective dissolution, the direct application of lacustrine phytolith assemblages for precipitation reconstruction may introduce significant bias. To address this, an empirical calibration coefficient of 0.6 was applied to the phytolith-mean annual precipitation (MAP) transfer function for these desert lakes, enabling precipitation estimates from the BRY core sediments to closely align with meteorological data. Thus, paleoenvironmental reconstructions based on phytolith assemblages from arid desert lake sediments should account for the effects of local hydroclimate and lake water pH on their environmental significance. This study enhances the reliability of paleoenvironmental reconstructions based on phytolith assemblages.