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.