Abstract For tacho-less order tracking, it is crucial to achieve an accurate estimation of instantaneous phase and frequency under non-stationary conditions for fault diagnosis of mechanical systems. Therefore, an instantaneous frequency estimation method based on dynamic time warping for rotating machinery was proposed. Firstly, a mono-component signal is obtained by variational mode decomposition of multi-harmonic vibration signal generated in practical engineering. Then, a stationary reference signal is constructed by the mean frequency of the vibration signal, which is obtained by the signal spectrum. Aligning the vibration signal with the reference signal to obtain the rough phase estimation and warping path. Finally, a polynomial model is constructed to calculate the analytic expression of the smooth warping path to obtain the instantaneous frequency result. The simulation and experiment present that the dynamic time warping-based method can estimate the instantaneous frequency of the signal under non-stationary conditions. Compared with the classical Hilbert transform method, the proposed dynamic time-warping algorithm has stronger noise resistance.