The invention provides a water toxicity analysis method based on a biologic omics integrated technology, belonging to the field of water toxicity assessment. The method comprises the following steps: selecting a tested water sample and a model animal to perform contamination experiment, collecting and extracting total RNA (ribonucleic acid), collecting a serum sample, and performing transcriptome detection on the RNA sample by adopting a gene chip to obtain whole genome expression data of the tested animal; performing nuclear magnetic resonance detection on the serum sample to obtain a nuclear magnetic resonance spectrogram and a serum metabolin signal; screening a differential expression gene according to gene expression magnification, and screening a differential expression metabolin according to a partial least squares method discriminate analysis result; and respectively performing biological pathway analysis based on transcriptome and metabolome so as to finally recognize the simultaneously changed biological pathways in the transcriptome and the metabolome. According to the method, the complex toxicity and mechanism of toxication of the polluted water can be tested and analyzed in high throughput, the full and correct bioinformatics parameters and indexes can be provided, and the processing on high throughput bioinformatics data is simplified.