In this study, measurement of thermal conductivity of multilayer thin dielectric film has been conducted via differential $3omega$ method. Also, verification of differential $3omega$ method has been accomplished with various proposed criteria. The target film for the measurement is 300 nm thick silicon dioxide which is covered with upper protective layer of various thicknesses. The upper protective layer is inserted between the target film and the heater line for purpose of electrical insulator or anti-oxidation barrier since the target film may be a good electrical conductor or a well-oxidizing material. Since the verification of differential $3omega$ method has not been conducted yet, we have shown that the measurement of thermal conductivity of thin films with upper protective layer via differential $3omega$ method is verified to be reliable as long as the proposed preconditions of the samples are satisfied. Experimental results show that the experimental errors tend to increase with aspect ratio between thickness of the upper protective layer and width of the heater line due to heat spreading effect.