Compound-specific hydrogen and oxygen isotope analyzes on leaf wax-derived n-alkanes (δ²H_n–alkane) and the hemicellulose-derived sugar arabinose (δ¹⁸O_ara) are valuable, innovative tools for paleohydrological reconstructions. Previous calibration studies have revealed that δ²H_n–alkane and δ¹⁸O_ara reflect the isotopic composition of precipitation, but – depending on the region – may be strongly modulated by evapotranspirative enrichment. Since no calibration studies exist for semi-arid and arid Mongolia so far, we have analyzed δ²H_n–alkane and δ¹⁸O_ara in topsoils collected along a transect through Mongolia, and we compared these values with the isotopic composition of precipitation (δ²H_p–WM and δ¹⁸O_p–WM, modeled data) and various climate parameters. δ²H_n–alkane and δ¹⁸O_ara are more positive in the arid south-eastern part of our transect, which reflects the fact that also the precipitation is more enriched in ²H and ¹⁸O along this part of the transect. The apparent fractionation ε_app, i.e., the isotopic difference between precipitation and the investigated compounds, shows no strong correlation with climate along the transect (ε_{2H n–C29/p} = −129 ± 14‰, ε_{2H n–C31/p} = −146 ± 14‰, and ε_{18O ara/p} = +41 ± 2‰). Our results suggest that δ²H_n–alkane and δ¹⁸O_ara in topsoils from Mongolia reflect the isotopic composition of precipitation and are not strongly modulated by climate. Correlation with the isotopic composition of precipitation has root-mean-square errors of 13.4‰ for δ²H_n–C29, 12.6 for δ²H_n–C31, and 1.2‰ for δ¹⁸O_ara, so our findings corroborate the great potential of compound-specific δ²H_n–alkane and δ¹⁸O_ara analyzes for paleohydrological research in Mongolia.