Many studies have involved the isolation and identification of allelochemicals from aquatic plants, but the algicidal properties of terrestrial plants have received less attention. This study aims to identify allelochemicals of ethyl acetate extracts from three plant materials (shaddock peel, pomegranate peel, pomegranate seed) and to investigate their inhibitory effects on Microcystis aeruginosa. The ethyl acetate extracts of the three plant materials were identified by GC-MS. Finally, 19 kinds of compounds (including organic acids, ester, ketone, sterol, etc.) were obtained and eight kinds of organic acids and N-phenyl-2-Naphthalenamine were proved to be allelochemicals. The inhibitory effects of the ethyl acetate extracts were also explored by M. aeruginosa bioassay. This showed that the inhibition percentages of ethyl acetate extracts of the three plant materials on the growth of M. aeruginosa were 43.9%, 47.5%, and 40.3%, respectively, when the algae were treated at a dosage of 20 mg/L extracts.