Evaluation of the concrete behavior in elevated temperatures is important in terms of first, structural construction safety under specified loadings, and second, measuring the loading capacity to continue operation. Furthermore, concrete behavior at high temperatures is strongly affected by microstructure. The calcium silicate hydrate (C–S–H), a nanostructure which is produced by hydration of cement paste, plays a significant role in enhancing the concrete strength under the impression of thermal fluctuations. Hence, this study investigates the microstructural performance of concrete exposed to high temperatures with a special focus on C–S–H nanostructure. Accordingly, 300 samples were cured for 1, 3, 7, 14, and 28 days in a moist room and then exposed to temperature range of 25–900°C for 2 h to investigate changes in their weight, length, compressive strength, and cracking behavior. Besides evaluating the microstructural behavior of the specimens in different temperatures, several techniques such as SEM, EDX, and XRD have been employed. Based on the results, any changes in the samples’ length, weight, and compressive strength depend on the C–S–H nanostructure behavior. In fact, following water decomposition from the C–S–H nanostructure at 900°C, the structure is partially converted to porous ceramic. These structural changes have caused a decline of 79–100% of the compressive strength. The compressive strength has decreased from 27.6 MPa to about 6 MPa. Also, the weight loss percentage of 28-days-old sample at this temperature was 18.84%. Based on the SEM and XRD results, this decline under high temperature arises due to the collapse of C–S–H nanostructure and formation of calcium oxide in the cement structure.