With the gradual emergence of customized manufacturing, intelligent manufacturing systems have experienced widespread adoption, leading to a surge in research interests in the associated problem of intelligent scheduling. In this paper, we study the flexible job shop scheduling problem (FJSP) with setup time, handling time, and processing time in a multi-equipment work center production environment oriented toward smart manufacturing and make-to-order requirements. A mathematical model with the optimization objectives of minimizing the maximum completion time, the total number of machine adjustments, the total number of workpieces handled and the total load of the machine is constructed, and an improved discrete particle swarm algorithm based on Pareto optimization and a nonlinear adaptive inertia weighting strategy is proposed to solve the model. By integrating the model characteristics and algorithm features, a hybrid initialization method is designed to generate a higher-quality initialized population. Next, three cross-variance operators are used to implement particle position updates to maintain information sharing among particles. Then, the performance effectiveness of this algorithm is verified by testing and analyzing 15 FJSP test instances. Finally, the feasibility and effectiveness of the designed algorithm for solving multi-objective FJSPs are verified by designing an FJSP test example that includes processing time, setup time and handling time.