Nowadays, stepping motors are usually used as precise actuators in various new scientific fields, such as syringe pumps, blood analyzers, and bio-3D printers. Controlling rotation of the stepping motor without speed fluctuation under no-load conditions plays an important role in improving the accuracy of the machine’s drive. This paper proposes a digital control method for a five-phase hybrid stepping motor. The proposed controller includes an original control loop and a PI adaptive integration gain control loop. The original digital control loop is redesigned from the analog controller by using the direct PIM method. The PI adaptive control loop is added to the original control loop in a parallel way to remove a steady deviation of the motor and suppress a physical saturation factor inside the plant. Lyapunov stability theory is used to prove a stability condition of the PI regulator gains. Experimental results show that the proposed controller can suppress the chattering caused by the switching structure and gives performances as good as that of the commercial analog controller in a high rotation speed range without fluctuation.