The thermal conductivity of silicon dioxide thin film covered by additional protective layer, silicon nitride, is measured by differential 3 omega method. This method needs the deposited metal line as a heater on the thin film of interest, but the upper layer should be inserted inevitably between heater and thin film in some cases; when the thin film is a welloxidized material or an electrically conductive material, the additional layer is need as a protective layer against oxidation or a insulator from current leakage. However, the verification of using differential 3 omega method for these cases had not conducted. In this paper, using differential 3ω method is verified to be reliable when the thermal conductivity of thin film with protective layer is measured as long as the conditions of the upper layer are satisfied and the requirements are proposed. Experiments show that the error of measurement experiment increases as the aspect ratio between upper layer thickness and heater rises i.e., the thickness of the upper layer increases.