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According to the characteristics of the flexible job shop scheduling problems, an optimization model is established with the goal of minimizing the completion time, and a hybrid algorithm of fruit fly optimization algorithm and genetic algorithm (FOA-GA) is proposed. In the olfactory stage, local search technique is used to find the optimal path; In the visual stage, combining the crossover and competition mechanism of genetic algorithm, the information exchange between individuals is carried out, the mutation operator with an optimization tendency and the conventional mutation operator are used to carry out the two-part mutation, and then the adaptive dynamic transfer operator is introduced to accelerate the convergence rate. In the simulation, the results of FOA-GA algorithm are compared with those of fruit fly optimization algorithm and genetic algorithm to prove its feasibility and effectiveness.