As the pulse train repetition ratio and pulse range are dominant factors, they achieve high treatment and high energy density. Achieving precise control according to purpose of treatment and diagnosis is important. A method for controlling the action time and changing the pulse train repetition range is used mainly through the output pulse of transcranial magnetic stimulation. The 32bits S3C2440 microprocessor was grafted to achieve safe control of circuit operation. Transcranial magnetic stimulation was operated through the power device and control section and research was carried out on the motion and output characteristics of transcranial magnetic stimulation according to the current pulse waveform and pulse train of the stimulation coil. As a result, the transcranial magnetic stimulation output efficiency was reduced and the transcranial magnetic stimulation output showed a regular increase of 50W according to the increase in pulse train repetition rate as pulse repetition rate was increased by 10 Hz from 10Hz to 60 Hz with a condenser charged voltage of 1,800V and 1,900V. This study introduces a treatment Pulse using Transcranial Magnetic Stimulation for changing various bacteria caused by rat head. One can obtain good changing characteristics of various bacteria by adjusting the charging voltage, the treatment pulse forming and the magnetic field inducing time.