Because a production logistics system is very complex and dynamic, optimizing its layout accurately and efficiently is difficult and even impossible based on the traditional mathematical method. This paper focus on finding the bottleneck issues in production logistics system and optimizing its layout based on Flexsim software. With an actual case of production logistics system, we can find the pivotal issues based Flexsim software. And then, we can't simulate continuously the production logistics system layout s with the equipment number or different layouts based on Flexsim, until the bottleneck disappears or is not so obvious. Finally we can obtain the improvement layout which meets with the requirement of enterprises' production plan preferably. The results prove that it is convenient and effective to simulate and optimize the production logistics system layout based on Flexsim.