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This paper discusses the optimization of printed circuit board (PCB) assembly scheduling for a large parallel system, JUKI FX-1, which is known as the most complicated PCB assembly machines. This whole problem is formulated and divided into nozzle allocation, feeder arrangement and component placement sequence three sub-problems. By analyzing the characteristics of the solutions, three heuristic algorithms, cluster analysis, sequence traversal, and assignation of built-in pick-and-place set, for solving the three sub-problems are designed, respectively. Then they are organically integrated according to their internal interrelation. The integrated algorithm was implemented on real life problems, and contrastive results showed that the proposed scheduling algorithm is more efficient than the software built-in JUKI FX-1.