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Measurement of electrical conductivity of conductive thin film deposited on a conductive substrate is important and challenging. An effective conductivity model was constructed for a bilayer structure to extract thin film conductivity from the measured Q-factor of a quasi-optical resonator. As a demonstration, aluminium films with thickness of 100 nm were evaporated on four silicon wafers whose conductivity ranges from ~10¹ to ~10⁵ S/m (thus, the proposed method can be verified for a substrate with a wide range of conductivity). Measurement results at ~180 GHz show that average conductivities are 1.66 × 10⁷ S/m (which agrees well with direct current measurements) with 6% standard deviation. The proposed method provides a contactless conductivity evaluation method for conductive thin film deposited on conductive substrate which cannot be achieved by the existing microwave resonant method.