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The paper presents a modelling of temperature distribution in the sandwich thermally isolated structures used in thermal microsensors. The two cases are considered: 1) the temperature distribution along the thickness of a thermally isolated structure; 2) the temperature distribution over the area of a thermally isolated structure. The basis for modeling is the eigenfunction method which is modified for the structure including several regions with homogeneous parameters. The model is applied to the concrete microsensors with sandwich thermally isolated structure. The relative error in determining the temperature distribution in replacing the two-layer structure (Si/SiO2) by the structure with homogeneous parameters is evaluated. The temperature distributions in the regions with the thermopiles and heater and along the line of disposition of hot thermojunctions of the thermopile are determined.