MEMS structures generally have been fabricated using surface-machining method, but the interface failure between silicon substrate and evaporated thin film frequently takes place due to the residual stress inducing by the applied the various loads. And the very important physical property in the heated environment is the linear coefficient of thermal expansion. Therefore this paper studied the residual stress caused the thermal loads in the thin film and introduced the simple method to measure the trend of the residual stress by the indentation. Specimens were made of materials such as Al, Au and Cu and thermal load was applied repeatedly. The residual stress was measured by nano-indentation using AFM and FEA. The existence of the residual stress due to thermal load was verified by the experimental results. The indentation length of the thermal loaded specimens increased minimum 11.8％ comparing with the virgin thin film caused by tensile residual stress. The finite element analysis results are similar to indentation test.