To evaluate the assembly sequence reasonably and ensure the validity of assembly sequence selection results, a fuzzy comprehensive evaluation method for assembly sequence was proposed. Firstly, the multi-objective evaluation index system of assembly sequence was constructed by survey and expert knowledge, and the quantification methods of each evaluation index were defined. Then the fuzzy analytic hierarchy process method was used to evaluate the relative relation among the indexes so as to obtain more accurate weight of each evaluation index of the assembly sequence. Finally, the initial value of each index of the feasible assembly sequence was calculated according to the quantization method of the evaluation index. Combining the relative weights of indexes, the advantages and disadvantages of the different assembly sequences were evaluated by means of elimination and choice translating reality, and according to the result of priority and inferiority, the best assembly sequence was selected. Taking an assembly sequence optimization process of X axis of a machine tool transmission system in an enterprise as an example, the feasibility of the proposed approach is illustrated. This result shows that the comprehensive evaluation result of feasible assembly sequence is reasonable, and the optimized scheme has better precision and efficiency. The multi-objective comprehensive evaluation method of assembly sequence is simple and practical, and the evaluation result is reasonable.