Subject to magnetic saturation, temperature rise, and other factors, the electrical parameters of permanent magnet synchronous motors (PMSMs) in marine electric propulsion systems exhibit time-varying characteristics. Existing parameter identification algorithms fail to fully satisfy the requirements of high-performance PMSM control systems in terms of accuracy, response speed, and robustness. To address these limitations, this paper introduces multi-innovation theory and proposes a novel multi-innovation extended Kalman filter (MIEKF) for the identification of key electrical parameters of PMSMs, including stator resistance, d-axis inductance, q-axis inductance, and permanent magnet flux linkage. Firstly, the extended Kalman filter (EKF) algorithm is applied to linearize the nonlinear system, enhancing the EKF’s applicability for parameter identification in highly nonlinear PMSM systems. Subsequently, multi-innovation theory is incorporated into the EKF framework to construct the MIEKF algorithm, which utilizes historical state data through iterative updates to improve the identification accuracy and dynamic response speed. An MIEKF-based PMSM parameter identification model is then established to achieve online multi-parameter identification. Finally, a StarSim RCP MT1050-based experimental platform for online PMSM parameter identification is implemented to validate the effectiveness and superiority of the proposed MIEKF algorithm under three operational conditions: no-load, speed variation, and load variation. Experimental results demonstrate that (1) across three distinct operating conditions, compared to forget factor recursive least squares (FFRLS) and the EKF, the MIEKF exhibits smaller fluctuation amplitudes, shorter fluctuation durations, mean values closest to calibrated references, and minimal deviation rates and root mean square errors in identification results; (2) under the load increase condition, the EKF shows significantly increased deviation rates while the MIEKF maintains high identification accuracy and demonstrates enhanced anti-interference ability. This research has achieved a comprehensive improvement in parameter identification accuracy, dynamic response speed, convergence effect, and anti-interference performance, providing an electrical parameter identification method characterized by high accuracy, rapid dynamic response, and strong robustness for high-performance control of PMSMs in marine electric propulsion systems.