A genetic-particle swarm optimization algorithm of multilayer-coded is proposed to solve the flow shop’s optimizing control problem of machinery industry. The objective of the issue is to minimize the production time. Through analyzing the actual machining conditions, control mathematical model of production line is set up. The algorithm bases on particle swarm algorithm and combines the genetic swarm optimization with the multilayer-coded mechanism. The algorithm has a higher speed and is used to avoid being trapped into local minima. The results show that the multilayer-coded genetic-particle swarm optimization algorithm has saved 9% times from the basic genetic algorithm. It has advantages of improving utilization ratio and production efficiency in machining line.