To solve the problems of low utilization rate of manufacturing resources, long non-processing time and difficult scheduling in a “research and production mixed line” workshop, a flexible job shop dual resource scheduling problem considering fixture loading and unloading is proposed. Firstly, the mathematical optimization model of the problem is established to minimize the makespan and setup time. Then, a non-dominated sorting genetic algorithm is proposed to solve it. The decoding algorithm to reduce setup time is designed to balance the two objectives. The operator is randomly selected from the crossover operator pool and the mutation operator pool, and the next generation is selected according to the non-dominated level and the congestion degree. Finally, the results of numerical experiment show that the proposed algorithm can solve the problem effectively.