A method for determining the complex permittivity of substances by the electromagnetic (EM) waveguide method in the microwave range using electrodynamics and the theory of multilayer dielectric structures is considered. The expression for the complex reflection coefficient of an EM wave in a waveguide with a substance sample is studied. Calculations of the dielectric constant of substances are carried out by analytical and numerical methods using computers. To obtain the desired complex permittivity of a substance, we use the relationship between the expression for the reflection coefficient modulus and the value of the standing wave coefficient over voltage measured in advance in the frequency range. The method is suitable for automation and application in enterprises producing and using fuels, construction and agricultural products. From the found value of the dielectric constant, the quality of substances can be determined. For example, the results of determining the dielectric constant several coals and solid-state foam are given.