Nowadays, geothermal energy could play an important role and source of renewable energy in replacing fossil fuels. In order to exploit effectively this potential, the suitable applied methods, and objectives need to have precise measurements to reconstruct the paleogeothermal history and evaluate the potential and stability (lifetime) of the geothermal system. Clay minerals provide the most important keys to solve the problems because clay minerals are the most abundant minerals group in geothermal systems. They can be used largely to interpret the physical-chemical conditions, isotope tracing, age, and evolution of a geothermal field. Especially changes in the interstratified clay structures (illitization, chloritization) present sensitive indicators to reconstruct evolution in either temperature and/or chemical environment. Moreover, the irreversible organic matter maturity supports the evolution of the sedimentary basin (maximum rate of sedimentation, burial, tectonic diagenesis, compaction, migration of fluids, thermal anomalies). Due to the different kinetics of organic matter and clay mineral reaction progress, different steps of the thermal history of sedimentary rocks can be distinguished. Thus, the combination of the methods allows the reconstruction of geothermal gradients and reciprocal heat flow conditions. Finally, clay minerals and organic matter studies therefore can help to better understand the paleogeothermal history of geothermal systems as well as give basic data for numerical models.