In the past the machinery used in punching of flexible printed circuit boards(FPCBs), it used mostly the rotary motor as the power source in the mechanism design. To transfer rotary motion to linear motion need a succession of mechanical conversion components, in order to achieve the purpose of linear output. However these mechanical parts for transforming bring some unavoidable problems such as the machinery itself huge volume, backlash and friction which created during the action process, all have harmful influences on the system dynamic performance and precision. Voice coil actuator has direct-drive output, high response and high thrust force these characteristics, therefore this research apply voice coil actuator to the punching of flexible printed circuit boards. For present industry, S-curve velocity profile is often used in point-to-point displacement intermittent action applications, due to its jerk-limited characteristic for reducing vibration and raising precision. Then integrating plans of S-curve velocity profile with voice coil actuator based on punching characters, to analyze the whole system dynamic performance in such a vertical linear output application. Then generalizing the dependence of influence factors of punching quality and motion characteristics of punching mechanism through experimental results. The achievement of this research could provide references for some related designers using similar linear actuators in vertical linear output applications.