Carbon fibre-reinforced polymer composites are widely used in modern aircraft structures for the high stiffness-to-weight ratio. An aircraft's exterior is commonly applied with coatings for minimisation of aerodynamic drag, resistance to chemicals, hydraulic fluid and ultraviolet exposure. The issues with the coatings are the possible high thickness variations due to the manual painting adopted. The existing thickness measurement methods are mostly suited to metals and cannot be well employed for in-field tests of composites. Here a new microwave cylindrical cavity resonator sensor is developed for the non-destructive thickness evaluation of coatings on composite substrates. The open cavity and conductive composite form a resonant system, where the presence of coating affects the surface impedance, causing changes in the resonance frequency. Applying the wall impedance perturbation and transmission line theories, an analytical model is proposed. From the measured data, a linear relationship is obtained between the resonance frequency shift and thickness change, thereby simplifying the prediction process. The insensitivity to the dielectric properties of the coating and anisotropy of the composite substrate offers convenient calibration and implementation. The new sensor can provide efficient on-site assessment of paint coatings on carbon fibre composite surfaces used in modern aircraft construction and other engineering applications.