A headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS) method was established to compare the difference of volatile substances of Microcystis at different growth periods. According to the ion mobility spectrum, the volatile organic compounds were compared by using chemometrics. The change patterns in the relative content of volatile compounds were observed by its fingerprint spectrum. The results show that there is obvious distinction in GC-IMS spectrum of volatile components, with the cumulative contribution rate of first two principal components being 78.2%. 91 volatile components are identified from Microcystis bloom samples, including 23 aldehydes, 21 alcohols, 16 esters, 10 ketones, 7 thioethers, 2 acids and 2 terpenes. Among them characteristic volatile components during Microcystis bloom include1-butanol, (E,E)-2,4-decadienal, acetic acid, dimethyl sulfi-de, (E)-3-hexene-1-alcohol,1-octene-3-one. This method is simple, rapid and sensitive. It can be used as a screening and confirmation method of volatile metabolites in water during algal bloom, thus providing data support for environmental monitoring.