The two-cylinder drive is one of many commonly used mechanical drive forms. Its synchronous control accuracy determines the movement accuracy of the working machinery. The paper established the mathematical model for the two-cylinder electro-hydraulic servo synchronous drive system, and revealed that the two-cylinder horizontal electro-hydraulic synchronous drive system has the cascade form of the linear system with the nonlinear system. Taking the band sawing machine and the broaching machine as the application object, the paper analyzed their compositions and synchronization CNC systems. Aiming at the dual-cylinder drive form for the broaching machine, the IPSO-PID synchronous controller of the two-cylinder system was designed. Through the digital simulation and actual testing, the results show that the IPSO-PID synchronous controller is faster in the tracking response speed and better in the synchronization performance than the conventional PID synchronization controller.