Aimed at the mechanical fault of CNC machine tool leading to the decline in the quality of machining and the degradation of system performance, the fault analysis method of CNC machine tool based on fuzzy comprehensive evaluation and failure modes and effects analysis (FMEA) was proposed. The thorough analysis was carried on using the FMEA for various types of fault of the machine, which were classified according to the hardware method of FMEA to obtain failure mode of key parts. The way of expert survey table was used to determine the severity of each fault(S), frequency(O), and detectability(D). The theory of fuzzy comprehensive evaluation was introduced to classify hierarchies membership degree of risk priority number of qualitative FEMA, and the secondary fuzzy evaluation model was established. The mechanical fault of the main shaft system and feed system were carried on the quantitative analysis. The results show that the comprehensive evaluation value after the blur is 8508, analysis of which verifies the validity of fuzzy comprehensive evaluation and FMEA on comprehensive analysis of the mechanical fault of CNC machine tool, which provide the complete effective safeguard for the selection of test points of CNC machine tool.