Cordyceps sinensis is one rare medicinal fungus produced in the Qinghai-Tibetan Plateau. Its quality and price varies hugely with different habitat, and its numerous substitutes have sprung up in functional food markets. This paper aims to discriminate the geographic origin of wild C. sinensis and its substitutes via the element analyzer-isotope ratio mass spectrometry and gas chromatography-isotope ratio mass spectrometry. The δ¹³C values of major fatty acids in the lipids of Cordyceps sinensis are characterized unanimously by the variation relation C_18:0 ﹤ C_18:2 ≈ C_16:0 ﹤ C_18:1; while their fluctuation intervals are notably different between those of neutral and polar lipids. The comparative analysis of the δ¹³C ratios of major fatty acids in lipids of Cordyceps sinensis suggests that the δ¹³C patterns may be sensitive potential indicators to discriminate its geographical origin. The δ¹³C values of individual major fatty acids of lipids from the cultivated stromata of Cordyceps militaris (SCM), the fermented mycelia of Hirsurella sinensis (FMH) and Paecilomyces epiali (FMP) range from −31.2‰ to −29.7‰, −16.9‰ to −14.3‰, and −26.5‰ to −23.9‰, respectively. Their δ¹³C pattern of individual major fatty acids may be used as a potential indicator to discriminate the products of natural C. sinensis and its substitutes.