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【Objective】This study aimed to comprehensively understand the metabolic differences of different tissues of water lily flowers to provide a theoretical basis for the precise application of water lily in the field of extraction, processing and functional food.【Method】Nymphaea ‘Panama Pacific’ was used to detect metabolites from petals, pistils and stamens by liquid chromatography-mass spectrometry（LC-MS）. The experimental data were analyzed by cluster analysis and multivariate statistical analysis. The specific metabolites of various tissues were searched by Kyoto encyclopedia of genes and genomes（KEGG）.【Result】A total of 1084 metabolites were detected from water lily flowers. The contents of metabolites in pistil, stamen and petal were significantly different. It was found that there were 553 differential metabolites between pistil and petal, 569 differential metabolites between pistil and stamen, and 613 differential metabolites between petal and stamen. In terms of dominant metabolite species, there were 138 dominant metabolites in petals, which were significantly enriched in 3 metabolic pathways: Biosynthesis of phenylpropanoids, flavonoid biosynthesis and citrate cycle. The dominant metabolites of pistils were 165,which were significantly enriched in 4 pathways including biosynthesis of phenylpropanoids, flavonoid biosynthesis, cyanoamino acid metabolism, nicotinate and nicotinamide metabolism. There were 206 dominant metabolites in stamens, which were significantly enriched in 3 metabolic pathways: Flavone and flavonol biosynthesis, biosynthesis of plant hormones, indole alkaloid biosynthesis. The contents of aspartic acid, tyrosine and glutamate in pistil were relatively high. And the contents of vincristine and tetrahydropalmatine in stamens were relatively high. Especially as a natural anticancer drug, the content of vincristine in stamens was about 1192 times that of pistils and 553 times that of petals, respectively.【Conclusion】The contents of metabolites in different tissues of water lily flowers are significantly different. The dominant metabolites of each tissue are significantly enriched in eight metabolic pathways, including phenylpropane biosynthesis, flavonoid biosynthesis, flavonoid and flavonol biosynthesis, and indole alkaloid biosynthesis. The non-targeted metabonomics technology can effectively screen the dominant metabolites in different tissues of lotus, and provide a scientific basis for the development and utilization of water lily flowers. [ABSTRACT FROM AUTHOR]