The invention belongs to the technical field of forensic medicine and biological medicine, and particularly relates to application of metabonomics in deducing submerging time of a corpse in water after early death. The marker for deducing the submerging time of the dead body in water is any one or a combination of more than one of the following 19 small molecule metabolites which are slightly influenced by the dead cause: epinephrine, cis-aconitic acid, citric acid, 1,2,3-cyclopropane tricarboxylic acid, riboflavin, citraconic acid, 4-acetylbutyric acid, D-glucosamine 6-phosphoric acid, phosphoenolpyruvic acid, 1-methyladenosine, 3-phosphoglyceric acid, creatine, carnosine, pyruvic acid, beta-alanine, 1, 5-diaminopentane, pantothenic acid, allantoin and 2-dimethylaminoguanosine. According to the method for deducing the submerged time of the dead corpse in the water based on the metabonomics marker, the early PMSI of the corpse in the water can be deduced conveniently and accurately, the influence of different causes of death and the judgment error of human subjective factors are greatly reduced, and more favorable help is expected to be provided for case detection in forensic practice.