To solve the machining line balancing problem for complicated prismatic parts, the execution sequence of operations should be considered during the line balancing process. After analyzing the constraints and optimization objectives, a method has been presented, which can provide optimal or near-optimal assignment of operations to the stations and sequence of operations inside the stations simultaneously. Based on the constraints of process and workstations, taking the tool change and rotation capabilities of machine center into consideration, this problem was modeled aiming at minimizing cycle time and cost of the line. Particle swarm algorithm was use to solve this problem. A heuristic decoder was designed for the algorithm to permutate each particle to a feasible line balancing plan. Pareto set was introduced to realize the multi-objective optimization and the algorithm efficiency was improved with elitist preserving strategy. Finally, a case was illustrated to prove the validity of the proposed method.