The mechanical resonance can be easily induced in the flexible transmission mechanisms in which high-stiffness servo systems are used. In order to improve the robustness of the system, the adaptive notch filter is often used, however, it will lead to mechanical resonance frequency deviation,therefore resonance suppression cannot be effectively realized. Based on this phenomenon, the influence to the mechanical frequency was quantitatively analyzed from the perspectives of system damping, discretization period and notch filter. The mechanism of mechanical resonance frequency deviation was analyzed in detail, and the core reason for resonance frequency deviation was revealed. It is concluded that the most effective notch frequency is still the natural resonant frequency (NTF) during resonance frequency deviation. Finally, simulation on MATLAB/Simulink and experiment verify the correctness and effectiveness of the conclusion and analysis.