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The innovative intelligent fuzzy weighted input estimation method (FWIEM) can be applied to the inverse heat transfer conduction problem (IHCP) to estimate the unknown time-varying heat flux of the multilayer materials as presented in this paper. The feasibility of this method can be verified by adopting the temperature measurement experiment. The experiment modular may be designed by using the copper sample which is stacked up 4 aluminum samples with different thicknesses. Furthermore, the bottoms of copper samples are heated by applying the standard heat source, and the temperatures on the tops of aluminum are measured by using the thermocouples. The temperature measurements are then regarded as the inputs into the presented method to estimate the heat flux in the bottoms of copper samples. The influence on the estimation caused by the temperature measurement of the sample with different thickness, the processing noise covariance Q, the weighting factor γ , the sampling time interval t Δ , and the space discrete interval x Δ , will be investigated by utilizing the experiment verification. The results show that this method is efficient and robust to estimate the unknown time-varying heat input of the multilayer materials. Keywords—Multilayer Materials, Input Estimation Method, IHCP, Heat Flux.