The microstructural changes in Co nanoparticles and an Au-10at.%Pd thin film have been investigated using an in situ heating holder with a micro-electro-mechanical system (MEMS). In Co nanoparticles, two phases (face-centered cubic and hexagonal closepacked crystal structures) were found to coexist at room temperature and microstructures at temperatures, higher than 1,000°C, were observed with a quick response time and significant stability. The actual temperature of each specimen was directly estimated from the changes in the lattice spacing (Bragg-peak separation). For the Au-10at.%Pd thin film, at a set temperature of 680°C, the actual temperature of the sample was estimated to be 1,020°C±123°C. Note that the specimen temperature should be carefully evaluated because of the undesired effects, i.e., the temperature non-uniformity due to the sample design of the MEMS chip, and distortion due to thermal expansion.