The invention relates to a comprehensive evaluation method of underground water, wherein the method includes steps of a, re-classifying the classification dividing value of seventeen water quality indexes such as manganese, fluoride, monoiodide and mercury in the underground water quality; b, selecting the water quality index participated in rating according to the testing index of the underground water sample, and substituting the testing result of the underground water sample and the classification dividing value of the selected water quality index participated in the evaluation to a membership function, and calculating and acquiring a fuzzy membership matrix; c, performing data conversion on a toxic index of the water quality index; d, according to the converted toxic index, the sample testing result, and the classification dividing value of the water quality index, calculating a weight matrix; e, coupling the fuzzy membership matrix with the weight matrix, and acquiring the evaluation result matrix and the evaluation grade of the underground water quality. The evaluation result fully considers about the risk of the human body health, and can comprehensively evaluate the underground water quality from the view of the human body health risk; the evaluation result can further objectively reflect the drinking safety.