System of diagnostics of the high-power electron accelerator based on undisturbing methods and measuring tools of electron beam characteristics as well as amplitude-time characteristics of the pulse forming system is presented. The analysis of amplitude-time characteristics reproducibility of the electromagnetic pulse formation system, electron beam spectral characteristics and properties of bremsstrahlung in the position of test specimen under given modes of operation of the accelerator performs using developed software. Possibilities of complex diagnostics of the power accelerator electron beams acceleration regime and accelerator units are illustrated by analysis of the accelerating tube parameters.