Abstract: Time synchronization of protective relay devices is essential for post-fault incident analysis and action tracing in new power systems. To address the limitations of incomplete clock monitoring coverage, reliance on manual synchronization correction, and lack of a unified management platform, this paper establishes a global clock desynchronization intelligent verification system for protective relay devices based on waveform recording data. Leveraging the existing master-slave waveform recording architecture, the system deploys an online monitoring unit for relay protection clock desynchronization at the master station, which centrally accesses wave recording data from multiple substations. Two schemes are designed, namely time-phased remote startup monitoring and homologous data comparison monitoring, to realize online monitoring of clock-offset of global protection devices under both fault and non-fault conditions. On this basis, the system incorporates a Kalman filtering intelligent verification algorithm with clock-offset–drift rate as state variables, which filters and predicts multi-time observation results while considering the influence of measurement noise to generate more accurate deviation verification values. Field applications demonstrate that the system can effectively identify desynchronized relays and maintain the post-synchronization clock deviation of devices within 20 ms, which is conducive to post-incident analysis and operation maintenance of clock synchronization status under relay protection device clock desynchronization.