In the paper, a 3D trajectory analysis taking into account the surface roughness of the thermionic cathode and thermal effects caused by its heating has been performed in the electron-optical system of a gyrotron with a frequency of 74,2 GHz and an output power of approximately 100 kW. A new approach based on the use of standard settings available in the 3D simulation software when the model parameters of thermionic emission being given, was used for consideration of the micron-sized cathode surface roughness. A comparison between the calculated and experimental data made it possible to clarify the regularities of the influence of the initial velocity spread and the change of geometry of the cathode assembly caused by its heating on the parameters of the electron beam formed in the electron-optical gyrotron system.