During the operation and ventilation of multiple air shafts in the mine, there are often disturbances between the air shafts, which in turn affects the ventilation safety of the mine. In this paper, taking the ventilation system of multi-air shaft combined operation mine as an example, according to the principle of safety system engineering and the theory of system evaluation, combined with the characteristics of multi-fan combined operation ventilation system, the evaluation index system of multi-air shaft combined operation ventilation system is established. The weight of each evaluation index is calculated by analytic hierarchy process, and the membership degree of evaluation factors is determined by expert scoring method. Finally, aiming at the safety of multi-air shaft combined operation ventilation system in mine, the qualitative evaluation is given by fuzzy comprehensive evaluation method. Taking Changping Coal Industry as an example, according to the constructed evaluation index system, the index weight is calculated, and the safety of the mine ventilation system is evaluated by fuzzy comprehensive evaluation. The results show that the safety level of the mine ventilation system is ' medium ' under the joint operation of multiple fans, which truly reflects the safety of the mine ventilation system and lays a foundation for the safe production of the mine.