The active engine mount (AEM) is developed in automotive industry to improve overall NVH performance. The AEM is designed to reduce major order of engine vibration over a broad frequency range, therefore it is of vital importance to extract major order signals from vibration before the actuator of the AEM works. This paper focuses on a method of real-time extraction of the major order acceleration signals at the passive side of the AEM. Firstly, the transient engine speed is tracked and calculated, from which the FFT method with a constant sampling rate is used to identify the time-related frequencies as the frequency base. Then the major order signals in frequency domain are computed according to the certain multiple relation of the frequency base. After that, the major order signals of acceleration can be reconstructed in time-domain, which are proved accurate through offline simulation, compared with the given signal. To verify the real-time performance of the method, a hardware-in-the-loop testing system based on MATLAB xPC target is established. LMS Data Acquisition System is adopted to track rotating speed online and extract major order signals offline. Both of the results are considered as the comparison with the online results from the hardware-in-the-loop testing system. It can be found that the method features high accuracy and satisfies the requirement of the real-time control of the AEM.