The work aims to overcome the limitations of the original rigid palletizers and improve the efficiency of cigarette palletizing in the tobacco logistics center. A flexible cigarette palletizing system based on multi-axis synchronous control technology was designed. With SIMATIC S7-1200 PLC as the control core, the system communicated with Kinco touch screen through PROFINET and connected 9 stepper motor drivers and sensors with the external input and output modules of PLC. The data sent by the IPC were processed by the PLC and synchronized by master control to achieve the synchronization of the flexible palletizers and complete the simultaneous grasping of diversified cigarettes. The stability and efficiency of the control system were verified by the experimental platform. The system could simultaneously adsorb 5 strips of cigarettes of different heights and widths, which greatly improved the efficiency of the cigarette palletizing robot. Compared to the rigid palletizing system, the flexible palletizing system increased the efficiency peak by about 24.9%. The designed system improves the efficiency of cigarette palletizing and increases the intelligence of tobacco packaging.