The pulsed magnets power supplies systems to affect injection and extraction of the electron beam have been realized for the Taiwan Photon Source (TPS) and Taiwan Light Source (TLS). The control systems of these pulsed magnets power supplies have been achieved as the well operation interfaces. To accomplish higher reliability operation, the advanced real-time diagnostic toolkit of pulsed magnets power supplies has to be developed. The SoC (System-on-Chip) embedded waveform acquisition system has been designed, implemented and applied for inspecting the pulsed magnets power supplies during routine operation. This waveform acquisition system not only owns 125 MS/s sample rate, 50 MHz bandwidth and 14 bits resolution, but also supports the EPICS software framework for complete system integration. The acquired current transformer waveform has been extracted immediately specific characteristics for examining the status easily, and these values have been archived for long time observation. This paper reports the design, implementation and real-time data analysis of SoC embedded waveform acquisition system for pulsed magnets power supplies systems.