Aiming at the status quo that labeling machine can only complete the sector or round bottle type labeling function and the labeling rate is low in the domestic market, the ARM9-based multi-function labeling control system was designed. Based on the motion relationship, taking the frequency of conversion motor as a parameter, the motor stopping pulse offset and startup latency time reference were calculated. Combined with closed-loop control of servo motor, the start labeling position of the labels on the bottles was decided, making sure that the label had no relative sliding at time of labeling, so as to achieve the high quality of labeling. Through the analysis of data of labeling machines’ field test, in cases of labeling double sides of flat bottles, labeling round bottles continuously and positioning labeling shaped round bottles, at the labeling precision of ±1 mm, labeling speeds could reach 60 bottles/min, 30 bottles/min and 20 bottles/min, and standard rates of labeling machine could keep above 97.9%, 99.1%, 98.7%. Using ARM9 embedded system to replace traditional PLC system, this system was used widely, with rapid response, high real-time manner and friendly interface, which did not only reduce the equipment cost, but also ensured the higher precision of labeling. The system can be widely used in various types of bottle label control.