Rotor speed fluctuation causes non-stationary instantaneous phase, while key-phasor signal jitter leads to reference phase drift. The superposition of these interferences significantly increases the error of synchronous phase measurement, severely restricting the dynamic identification and balancing of rotor systems. To address this issue, a tracking regression method based on instantaneous phase resampling is proposed for high-precision synchronous phase measurement under complex operating conditions. First, the instantaneous phase of the vibration signal is calculated via zero-phase shift wideband bandpass filtering and the Hilbert transform to fully extract the rotor′s speed fluctuation information. The instantaneous phase is then tracked and resampled using an interpolated and up-sampled key-phasor sequence, leveraging the key-phasor signal to mitigate the phase non-stationarity caused by speed fluctuation. A first- and second-order cyclostationary model is constructed to accurately describe the resampled phase, which quantifies the key-phasor jitter interference as additive noise. Furthermore, linear regression is applied to the resampled phase to effectively suppress this noise, and an asymptotically unbiased estimate of the intercept yields a precise measurement of the synchronous phase. Finally, the superior antiinterference capability of the method is evaluated through simulations and experiments. Simulations show phase errors were reduced by 70.4% and 40.5% compared to conventional methods. Experiments demonstrate <2° phase fluctuation under strong noise, enabling a 92.2% vibration reduction in a single balancing run. The method provides a robust solution for high-precision phase measurement under complex interferences, supporting applications like rotor fault diagnosis and dynamic balancing.