To address the issue of mechanical resonance frequency detection in dual-inertia servo systems, this paper proposes an online identification method for mechanical resonance frequency using a low-pass filter and cascaded second-order generalized integrator—frequency-locked loop (LPF-CSOGI-FLL). Initially, the cascaded second-order generalized integrator—frequency-locked loop (CSOGI-FLL) is employed to eliminate the interference of direct current (DC) bias in resonance frequency identification. From a dual-stage structural perspective, the first second-order generalized integrator (SOGI-FLL) acts as a band-pass pre-filter to extract the mechanical resonance signal from the signal to be tested. The second SOGI-FLL generates a signal with equal amplitude and frequency to the mechanical resonance and obtains the frequency of the resonance signal through the frequency-locked loop. Subsequently, a low-pass filter (LPF) is applied to the frequency feedback loop of the second-stage SOGI-FLL, effectively reducing the oscillation of the estimated frequency. Finally, combining the CSOGI-FLL with an LPF forms a novel structure, namely, LPF-CSOGI-FLL. The results demonstrate that the proposed method significantly improves the detection accuracy of mechanical resonance frequency under various conditions. Compared to traditional offline techniques, this method overcomes the impact of resonance frequency drift and enhances system stability.