Micro-stepping motion of ultrasonic motors satisfies biomedical applications, such as cell operation and nuclear magnetic resonance, which require a precise compact-structure non-magnetization positioning device. When the pulse number is relatively small, the stopping characteristics have a non-negligible effect on the entire stepwise process. However, few studies have been conducted to show the rule of the open-loop stepwise motion, especially the shutdown stage. In this study, the modal differences of the shutdown stage are found connected with amplitude and velocity at the turn-off instant. Changes of the length in the contact area and driving zone as well as the input currents, vibration states, output torque, and axial pressure are derived by a simulation model to further explore the rules. The speed curves and vibration results in functions of different pulse numbers are compared, and the stepwise motion can be described by a two-stage two-order transfer function. A test workbench based on the Field Programmable Gate Array is built for acquiring the speed, currents, and feedback voltages of the startup–shutdown stage accurately with the help of its excellent synchronization performances. Therefore, stator vibration, rotor velocity, and terminal displacements under different pulse numbers can be compared. Moreover, the two-stage two-order model is identified on the stepwise speed curves, and the fitness over 85% between the simulation and test verifies the model availability. Finally, with the optimization of the pulse number, the motor achieves 3.3 µrad in clockwise and counterclockwise direction.