The work aims to improve the electronic cam flying shear algorithm in the existing machine in order to enrich the packing types of pillow packing machine and improve its packing precision and efficiency. According to the process flow of pillow packing machine, the mathematical model of electronic cam flying shear was established, and the quintic polynomial motion control algorithm was designed to realize the coordinated and synchronous operation of feeding shaft, film feeding shaft and cutter shaft. Then, the control system was designed. According to the test results, with the increase of the packing speed and decrease of packing length, the qualified packing rate was reduced, but the electronic cam curve designed by the quintic polynomial planning had good continuity and flexibility, avoiding the rigid and mechanical vibration. Within the allowable error of ±1 mm, the qualified packing rate was always 100%, which effectively improved the control accuracy. The electronic cam curve designed completely meets the requirements of production technology. The actual test proves the reliability and stability of the control system based on electronic cam flying shear, and also proves the superiority of the motion control algorithm.