Aiming at the distributed flexible job shop scheduling problem under dual resource constraints considering the influence of workpiece transportation time between factories and machines, a distributed flexible job shop scheduling problem (DFJSP) model with the optimization goal of minimizing completion time is established, and an improved mayfly algorithm (IMA) is proposed to solve it. Firstly, the mayfly position vector is discrete mapped to make it applicable to the scheduling problem. Secondly, three-layer coding rules of process, worker, and machine is adopted, in which the factory selection is reflected by machine number according to the characteristics of the model, and a hybrid initialization strategy is designed to improve the population quality and diversity. Thirdly, an active time window decoding strategy considering transportation time is designed for the worker–machine idle time window to improve the local optimization performance of the algorithm. In addition, the improved crossover and mutation operators is designed to expand the global search range of the algorithm. Finally, through simulation experiments, the results of various algorithms are compared to verify the effectiveness of the proposed algorithm for isomorphism and isomerism factories instances.