In the paper, modification of the electrophoretic light scattering (ELS) method for improving an accuracy of determining the electrophoretic mobility and zeta potential of nanoparticles in colloidal systems has been put forward. The modification included the creation of an original experimental setup operating in the heterodyne mode using a multimode fiber at the input of the recording unit, an increase in the signal-to-noise ratio of the system, and also an expansion of ranges of nanoparticles’ key parameters: sizes, electrical conductivity, concentration in solution. The theoretical substantiation for processing the scattering signal of polydisperse colloidal solutions of nanoparticles and calculating the electrophoretic mobility and zeta potential of colloidal systems was given. The high accuracy of the measured parameters was achieved, in comparison with the data obtained from the ZetaSizer Nano commercial device.