Emergencies such as machine breakdowns and rush orders greatly affect the production activities of manufacturing enterprises. How to deal with the rescheduling problem after emergencies have high practical value. Meanwhile, under the background of intelligent manufacturing, automatic guided vehicles are gradually emerging in enterprises. To deal with the disturbances in flexible job shop scheduling problem with automatic guided vehicle transportation, a mixed-integer linear programming model is established. According to the traits of this model, an improved NSGA-II is designed, aiming at minimizing makespan, energy consumption and machine workload deviation. To improve solution qualities, the local search operator based on a critical path is designed. In addition, an improved crowding distance calculation method is used to reduce the computation complexity of the algorithm. Finally, the validity of the improvement strategies is tested, and the robustness and superiority of the proposed algorithm are verified by comparing it with NSGA, NSGA-II and SPEA2.