Lipid extracts from a 61.7-cm-long subtropical stalagmite in southern China, spanning the period of ca. 10,000–21,000 yr ago as constrained by U–Th dating, were analyzed using gas chromatography–mass spectrometry. The higher plants and microorganisms in the overlying soils contribute a proportion of n-alkanes identified in the stalagmite. The occurrence of LMW (lower molecular weight) n-alkanols and n-alkan-2-ones in the stalagmite was mainly related to the soil microorganisms. We suggest that HMW (higher molecular weight) n-alkanols and n-alkan-2-ones identified in the stalagmite originate from soil organics and reflect input from contemporary vegetation. Shifts in the ratio of LMW to HMW n-alkanols or n-alkan-2-ones indicative of the variation of soil ecosystems (e.g., microbial degradation of organic matter and/or the relative abundance of soil microorganisms to higher plants) are comparable with the subtropical alkenone-SST (sea surface temperature) record of the same period. The similar trends seen in the δ13C data and the lipid parameters in this stalagmite imply that the overlying soil ecosystem response to climate might be responsible for the variation of δ13C values.