Various omics and their combined techniques have certain applications in the study of the mechanism of toxicity of Chinese materia medica, the screening of toxic biomarkers, and the prediction of the toxicity of Chinese materia medica. It has been found that the current application scope of exploring the toxicity of Chinese materia medica based on omics technology still needs to be expanded. In terms of organ damage caused by Chinese materia medica, omics technology is mostly used to study hepatotoxicity. In terms of the attenuation mechanism of TCM, proteomics and metabolomics have more advantages, and the two have potential prospects in exploring the processing or compatibility of TCM to reduce toxicity and increase efficiency. The combination of omics technology with network pharmacology, bioinformatics and other technologies is more conducive to providing references for the in-depth study of the toxicity of Chinese materia medica.