It exists in complexity and fuzziness in structure and failure character of engineering machinery complex system. To solve the problem, fuzzy theory was introduced into fault tree analysis, and then the steps, principles and methods of fuzzy fault tree are determined. Based on the analysis of engineering machinery typical engine systemic structure and fault criterion, a fuzzy fault tree is established. Used a fuzzy mathematics method of reliability analysis with fuzzy fault rate and the median method of fuzzy significance analysis, the fuzzy fault rate and fuzzy significance of parts and subsystems is calculated. The result indicates that this method can solve the fuzziness problem of failure criterion and data in fault tree analysis. The result provides valuable reference for the reliability analysis.