In order to inhibit the influence of the output signals of three-axis simulator exhibited the phase delays and noise on the performance of missile’s hardware-in-loop simulation system, a modified tracking differentiator which was used to filter and phase advance was analyzed and designed. Based on the principle of traditional tracking differentiator, the basic structure of tracking the output signals of threeaxis simulator was designed. Due to the differential signal obtained from the tracking differentiator trembles existed noise, the vibration phenomenon of the output signals was analyzed. On this basis, a design method that the differential signal cascaded another tracking differentiator was proposed to filter the signal pollution and output signals noise. Finally, as the examples of one missile’s hardware-in-loop simulation system which were the output signals of three-axis simulator exhibited the phase delays and noise, the performance of the system was verified by comparing with the lead correction method. Simulation results show that the attitude angular velocity can be extracted by the modified phase advancer efficiently, and the modified phase advancer possesses excellent filter and phase advanced performance, which prove the correctness and validity of the modified phase advancer in the hardware-in-loop simulation system for missile.