The cooling system of stimulating coils in transcranial magnetic stimulation system is important as the frequency and stimulating intensity increase in clinical trials. But the configurations of coils with different cooling systems are also different. These differences may cause variations in stimulating parameters. This paper compared the internal water cooled coil and the air cooled coil with same turns and inner diameters in aspects of waveform, magnetic field, induced electric field and focal area, when the coils were connected to the same main circuit. Results showed that the peak magnetic flux density and induced electric field were similar to each other. Compared to the air cooled coil, the internal water cooled coil had a smaller inductance, a larger stimulating current, a shorter pulse width, a shorter rise time and a smaller focal area. The internal water cooled coil is consequently suggested because of its better cooling efficiency, although there are some differences between this kind of coil and traditional air cooled coils.