Abstract: GC-IMS (gas chromatography-ion mobility spectroscopy) was used to analyze the differences between the volatile substances of two hosts of Cistanches deserticola in the Hotan area, Xinjiang. The results showed that 35 volatile substances were detected by GC-IMS, among which 27 volatile substances were identified qualitatively, including 8 aldehydes, 5 alcohols, 4 esters, and 1 ketone, predominantly aldehydes, and alcohols. There were obvious differences in the volatile substances of Cistanche deserticola between 'Red Willow' and 'Hoxylon'. The main substances that differed between the two were 2-phenylacetaldehyde, benzaldehyde, (E)-2-heptenal, 3-(Methylmercapto) propionaldehyde, 1-hexanal, heptanal, 3-methyl-2-butenal, acetic acid methyl ester, acetic acid hexyl ester, 1-hexanol, 3-hydroxy-2-butanone, 2-methyl-1-propanol, acetic acid ethyl ester. The two different hosts of Cistanche deserticola could be effectively distinguished by principal component analysis, and the cumulative variance contribution of PC1 and PC2 reached 91%. Meanwhile, by constructing the heat map of volatile substances clustering and fingerprinting, they can provide theoretical references for the identification of different hosts of Cistanche deserticola and the study of volatile substances.