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In flexible job shop scheduling problem (FJSP), the collision of bidirectional rail guided vehicles (RGVs) directly affects RGVs scheduling, and it is closely coupled with the allocation of production equipment, which directly affects the production efficiency. In this problem, taking minimizing the maximum completion time of RGVs and minimizing the maximum completion time of products as multi-objectives a dual-resource integrated scheduling model of production equipment and RGVs considering conflict-free routing problem (CFRP) is proposed. To solve the model, a multi-objective improved discrete grey wolf optimizer (MOID-GWO) is designed. Further, the performance of popular multi-objective evolutionary algorithms (MOEAs) such as NSGA-Ⅱ, SPEA2 and MOPSO are selected for comparative test. The results show that, among 42 instances of different scales designed, 37, 34 and 28 instances in MOID-GWO are superior to the comparison algorithms in metrics of generational distance (GD), inverted GD (IGD) and Spread, respectively. Moreover, in metric of Convergence and Diversity (CD), the Pareto frontier (PF) obtained by MOID-GWO is closer to the optimal solution. Finally, taking the production process of a construction machinery equipment component as an example, the validity and feasibility of the model and algorithm are verified.