The invention relates to a method for evaluating kidney toxicity of compounds through detecting the contents of creatinine in zebra fish tissues. The method is applied to kidney toxicity researches. In the researches that utilize a zebra fish embryo model to study the toxic effect of compounds on the kidney, the creatinine component in embryo tissues is extracted, then the creatinine content is measured through a LC-MS (liquid chromatography-mass spectrum) method, the creatinine content can be taken as a detection index for evaluating the embryo kidney functions, and thus a rapid and precise compound kidney toxicity evaluation system with strong specificity is built.