Currently, transcranial magnetic stimulation (TMS) has been widely used in the treatment of depression, Parkinson’s disease and other neurological diseases. To be able to monitor the brain’s internal activity during TMS in real time and achieve better treatment outcomes, the researchers proposed combining TMS with neuroimaging methods such as magnetic resonance imaging (MRI), both of which use Tesla-level magnetic fields. However, the combination of strong current, large magnetic field and small size is likely to bring physical concerns which can lead to mechanical and thermal instability. In this paper, the MRI static magnetic field, the TMS coil and human head model were built according to the actual situations. Through the coupling of the magnetic field and the heat transfer module in the finite element simulation software COMSOL, the force and temperature of the TMS coil and head were obtained when the TMS was used in combination with MRI (TMS-MRI technology). The results showed that in a 3 T MRI environment, the maximum force density on the coil could reach 2.51 × 109 N/m3. Both the direction of the external magnetic field and the current direction in the coil affected the force distributions. The closer to the boundary of the external magnetic field, the greater the force. The magnetic field generated by the coil during TMS treatment increased the temperature of the brain tissue by about 0.16 °C, and the presence of the MRI static magnetic field did not cause additional thermal effects. The results of this paper can provide a reference for the development of the use guidelines and safety guidelines of TMS-MRI technology.