This work aimed to classify Aspergillus (8 species, 28 strains) by using a secondary metabolite profile-based chemotaxonomic classification technique. Secondary metabolites were analyzed by liquid chromatography ion-trap mass spectrometry (LC-IT-MS) and multivariate statistical analysis. Most strains were generally well separated from each section. A. lentulus was discriminated from the other seven species (A. fumigatus, A. fennelliae, A. niger, A. kawachii, A. flavus, A. oryzae, and A. sojae) with partial least-squares discriminate analysis (PLS-DA) with five discriminate metabolites, including 4,6-dihydroxymellein, fumigatin, 5,8-dihydroxy-9-octadecenoic acid, cyclopiazonic acid, and neosartorin. Among them, neosartorin was identified as an A. lentulus-specific compound that showed anticancer activity, as well as antibacterial effects on Staphylococcus epidermidis. This study showed that metabolite-based chemotaxonomic classification is an effective tool for the classification of Aspergillus spp. with species-specific activity.