Wild Cordyceps sinensis (WCS) is considered to be one rare and valuable medicinal fungus for preventing and treating diverse chronic diseases, and its quality and price vary hugely with different producing areas. However, the determination of geographic origin has long been hindered by uncertainties of existing methods. Lately, it has been found that the fatty acid composition in lipids may be used to access geographic origin. Seventeen fatty acids were identified and their relative and absolute contents were measured by gas chromatography−mass spectrometry (GC−MS) in these samples with C_16:0, C_18:0, C_18:1 and C_18:2 as major constituents including linolenic acid (C_18:3) (1.02−4.83%). Total unsaturated fatty acids (75.74−90.87%) are evidently enriched compared with the other common fungi. Based on the specific fatty acid composition in lipids, the influences of environmental temperature and humidity on lipid synthesis in WCS are discussed, and the fatty acid profile and the ratio of C_18:1/C_18:2 in polar lipids are suggested to be two potential indicators for determination of geographical origin.