A method for identifying biological pathways of model animals affected by pollutants in water, the method comprising: 1) exposure experiment: collecting a water sample from polluted water, selecting model animals, administering the water sample to the model animals in an experimental group, and administering purified water to the model animals in a blank group; 2) sample collection: after a cycle of the exposure experiment, extracting total RNA samples of livers of the model animals; collecting blood samples of the model animals, and centrifuging the blood samples to obtain serum samples; 3) transcriptome detection: mixing every three RNA samples to yield one sample, conducting transcriptome microarray detection; providing three gene chips for the experimental group and the blank group, respectively; and conducting statistics analysis, whereby obtaining complete genome expression data of model animals; 4) metabolome detection: conducting nuclear magnetic resonance detection on the serum sample of each model animal of the experimental group and the blank group to yield NMR spectra of serum, whereby obtaining signal values of serum metabolites; 5) screening of differentially expressed genes: comparing gene expression signals of the experimental group with the gene expression signals of the blank group according to detection results by the gene chips; screening genes having an expression multiple > 2.0 and a false discovery rate < 0.1 as the differentially expressed genes; 6) screening of differentially expressed metabolites: performing segmental integral on the NMR spectra of serum, conducting partial least squares discriminant analysis (PLS-DA) on obtained integral data, and screening metabolites having variable influence on projection > 1.0 and FDR < 0.01 as the differentially expressed metabolites; and 7) identification of biological pathways: conducting biological pathway analyses of the transcriptome and the metabolome to identify pathways that have a hypergeometric test p < 0.05 and contain more than four differentially expressed genes as obviously affected transcriptome pathways and to identify pathways that have a pathway impact > 0.1 as obviously affected metabolite pathways, respectively, on the differentially expressed genes and differentially expressed metabolites; and identifying the biological pathways where both the transcriptome and the metabolome vary. 1) exposure experiment: collecting a water sample from polluted water, selecting model animals, administering the water sample to the model animals in an experimental group, and administering purified water to the model animals in a blank group; 2) sample collection: after a cycle of the exposure experiment, extracting total RNA samples of livers of the model animals; collecting blood samples of the model animals, and centrifuging the blood samples to obtain serum samples; 3) transcriptome detection: mixing every three RNA samples to yield one sample, conducting transcriptome microarray detection; providing three gene chips for the experimental group and the blank group, respectively; and conducting statistics analysis, whereby obtaining complete genome expression data of model animals; 4) metabolome detection: conducting nuclear magnetic resonance detection on the serum sample of each model animal of the experimental group and the blank group to yield NMR spectra of serum, whereby obtaining signal values of serum metabolites; 5) screening of differentially expressed genes: comparing gene expression signals of the experimental group with the gene expression signals of the blank group according to detection results by the gene chips; screening genes having an expression multiple > 2.0 and a false discovery rate < 0.1 as the differentially expressed genes; 6) screening of differentially expressed metabolites: performing segmental integral on the NMR spectra of serum, conducting partial least squares discriminant analysis (PLS-DA) on obtained integral data, and screening metabolites having variable influence on projection > 1.0 and FDR < 0.01 as the differentially expressed metabolites; and 7) identification of biological pathways: conducting biological pathway analyses of the transcriptome and the metabolome to identify pathways that have a hypergeometric test p < 0.05 and contain more than four differentially expressed genes as obviously affected transcriptome pathways and to identify pathways that have a pathway impact > 0.1 as obviously affected metabolite pathways, respectively, on the differentially expressed genes and differentially expressed metabolites; and identifying the biological pathways where both the transcriptome and the metabolome vary.