In the milling process, the friction and wear of the tooth minor flank of the square shoulder milling cutter directly affects the machined surface quality and the cutter’s life. The friction of the minor flank of the cutter tooth presents a nonlinear distribution, and its variation cannot be revealed by using a single parameter. It is difficult to identify the dynamic characteristics of the friction of the minor flank of the cutter tooth. In this work, the friction velocity model for the cutter tooth minor flank was developed by using the relative motion relationship between the flank area element and the workpiece transition surface. In accordance with the atomic excitation theory developed under the potential energy field at the friction interface of the cutter, the model for friction energy consumption under the friction velocity and thermal-stress coupling field on the minor flank of the cutter tooth was developed. Based on the mechanism of the interfacial atomic thermal vibration, the model for the friction coefficient under thermal-stress mechanical coupling was developed. Using the instantaneous friction coefficient and normal stress, the instantaneous friction distribution function of the flank was obtained. Finally, an identification method for the friction dynamic characteristics of the shoulder milling cutter tooth flank under vibration was proposed and verified by experiments.