This paper proposes an integrated framework that synergistically combines a phase-locked loop (PLL) and an enhanced extended Kalman filter (EKF) to address dynamic harmonic and interharmonic tracking challenges in rail transit power supply systems. In the proposed method, the PLL is employed to quickly and accurately lock the fundamental frequency, thereby providing a stable reference for the EKF. This significantly reduces the difficulty in tracking fundamental wave parameters within the EKF state model. A frequency drift constraint term is introduced to describe the unsteady characteristics of interharmonics, thereby improving the model’s adaptability to time-varying harmonics. Finally, by dynamically adjusting the process noise covariance matrix combined with the Sage-Husa adaptive algorithm, the anti-disturbance capability of the algorithm under complex working conditions such as traction load mutations and electromagnetic interference is enhanced. Experimental results indicate that under complex operating conditions where the fundamental frequency drifts and interharmonics are present, the algorithm proposed in this paper exhibits fast tracking speed and high accuracy for the amplitude and frequency of harmonics/interharmonics, making it highly suitable for online monitoring of harmonics/interharmonics in rail transit power supply systems.