With the development of industrial production, drive systems are demanded for larger inertias of motors and load machines, whereas shafts should be lightweight. In this situation, it will excite mechanical vibrations in load side, which is harmful for industrial production when the motor works. Because of the complexity of the flexible shaft, it is often difficult to calculate stiffness coefficient of the flexible shaft. Furthermore, only the velocity of driving side could be measured, whereas the driving torque, the load torque, and the velocity of load side are immeasurable. Therefore, it is inconvenient to design the controller for the uncertain system. In this paper, a low-order IP controller is designed for an uncertain two-mass torsional system based on polynomial method and time-frequency analysis (TFA). IP controller parameters are calculated by inertias of driving side and load side as well as the resonant frequency based on polynomial method. Therein, the resonant frequency is identified using the time-frequency analysis (TFA) of the velocity step response of the driving side under the open-loop system state, which can not only avoid harmful persistent startstop excitation signal of the traditional method, but also obtain high recognition accuracy under the condition of weak vibration signal submerged in noise. The effectiveness of the designed IP controller is verified by groups of experiments. Experimental results show that good performance for vibration suppression is obtained for uncertain two-mass torsional system in a medium-low shaft stiffness condition.