The nanopore formation process that occurs by supplying a thermal spike to single crystal CeO2 has been simulated using a molecular dynamics method. As the initial condition, high thermal energy was supplied to the atoms in a nano-cylinder placed at the center of a fluorite structure. A nanopore was generated abruptly at around 0.3 ps after the irradiation, grew to its maximum size at 0.5 ps, shrank during the time to 1.0 ps, and finally equilibrated. The nanopore size increased with increasing effective stopping power gSe (i.e., the thermal energy deposited per unit length in the specimen), but it became saturated when gSe was 0.8 keV/nm or more. This finding will provide useful information for precise control of the size of nanopores. Our simulation confirmed nanopore formation found in the actual experiment, irradiation of CeO2 with swift heavy ions, but could not reproduce crystalline hillock formation just above the nanopores.