An apparatus for measuring thickness in super-thin films consists of a special resonator unit in the form of an open-bottom cylinder which is connected to a microwave swept frequency microwave source via a decoupler and a matching unit installed in a waveguide that connects the resonator unit with the microwave source. The apparatus operates on the principle that thin metal film F, the thickness of which is to be measured, does not contact the end face of the open bottom of the cylindrical resonator sensor unit and functions as a bottom of the cylindrical body. The design of the resonator excludes generation of modes other than the resonance mode and provides the highest possible Q-factor. As the conductivity directly related to the film thickness, it is understood that measurement of the film thickness is reduced to measurement of the resonance peak amplitudes. This means that superhigh accuracy inherent in measurement of the resonance peaks is directly applicable to the measurement of the film thickness or film thickness deviations.