Abstract: The large growth of blue-green algae in water is an important cause of water eutrophication, so it is very important to inhibit the growth of blue-green algae in the application of in-situ ecological restoration. The growth of algae can be inhibited by some allelochemicals secreted by submerged plants. Qualitative and quantitative studies on allelopathic substances secreted by submerged plants and clarifying the action mechanism of allelopathic substances should have certain theoretical guidance and practical significance for ecological management of eutrophic water bodies. Five submerged plants, including Myriophyllum verticillatum, Vallisneria natans, Elodea canadensis, Hydrilla verticillata, and Ceratophyllum demersum, which were common in southern China, were selected and their hydroponic solution was analyzed by GC-MS. The species of secondary metabolites secreted by submerged plants were identified and their potential allelopathic effects were investigated. The results showed that a total of 56 compounds were detected in the hydroponic solution of 5 submerged plants, of which the most detected were organic acids. The contents of organic acids secreted by Myriophyllum verticillatum, Vallisneria natans, Elodea canadensis and Hydrilla verticillata were the highest, while the contents of ketones and esters were high in the hydroponic solution of Ceratophyllum demersum. It was speculated that the main allelochemicals detected in the hydroponic solution of Myriophyllum verticillatum were succinic acid, citric acid and phenol; lactic acid, citric acid, sebacic acid, stearic acid, lauric acid, and phenol in the hydroponic solution of Vallisneria natans played the main role of algae inhibition. The main allelochemicals were azelaic acid, p-hydroxybenzoic acid, and palmitic acid in the hydroponic solution of Elodea canadensis; nonanoic acid, ferulic acid, capric acid, oleic acid, butyl acetate and diisobutyl phthalate were the substances that played the role of decontamination and algae inhibition in the hydroponic solution of Hydrilla verticillata and Ceratophyllum demersum.