Abstract: In order to investigate the characteristics and differences of culture water planting floating bed water dropwort and reveal the mechanism of allelopathy and the crosstalk with microorganisms, it is necessary to study the metabolites in the culture water. The content of metabolites in the culture water planting the water dropwort of three different stages (proliferation stage, juvenile stage and adult stage) was quantified via LC-ESI-MS based non-targeted metabolomics technology. The primary metabolites and the metabolites with significant difference were identified through multivariate statistics and univariate statistics. The correlation analysis between important metabolites and environmental remediation was carried out. The results showed that: (1) 306 metabolites were detected in the culture water at different stages. The content ratios of 13 metabolites at each stage were above 1%. Among them, compounds like stearic acid, betaine and erucamide were the key metabolites for cold tolerance, allelopathy and denitrifying bacteria accumulation. (2) 112 metabolites were significantly different metabolites between stages, allelopathy metabolite stearic acid and plant-microbe crosstalk metabolite D-(-)-quinic acid were significantly different metabolites between any stages. (3) Correlation analysis results showed that the contents of 9 allelopathy metabolites, azelaic acid, myristic acid, catechol, 3, 5-dihydroxybenzoic acid, ferulic acid, salicylic acid, stearic acid, caffeic acid and benzoic acid were highly corelated (r > 0.6, P < 0.01) and the content was the highest in the juvenile stage. Taken together, at least 23 metabolites in the culture water are related to environmental remediation, 9 of them may work together during the allelopathy of water dropwort and water dropwort in the juvenile stage is more suitable for the developing of water dropwort algae inhibitor.