The work aims to design a multi-axis synchronous control system based on virtual shaft to improve the quality of bag making products and accuracy of synchronous control and achieve product technology upgrades. Taking the three-side sealing bag making machine as the research object, its technological process and working principle were introduced, its motion control system topology structure was built, the basic principle of multi-axis synchronous control of bag making machine was analyzed in detail based on the synchronous control strategy of virtual shaft, and a floating roller compensation algorithm was designed. The software design methods were given, and the experimental data were collected through actual operation for verification. The proposed control system could meet the motion control requirements of the bag making machine, and compensate the synchronization error between the adjacent two axes, so that the synchronization error between the two traction axes of the bag making system was controlled at about 0.3%. The synchronous control system with this strategy has good synchronization and stability, improves the quality, accuracy and efficiency of bag making, reduces the defective rate, and better meets the cutting precision requirements of bag making machine.