Pulse transformer has the advantages of high step-up ratio, good reliability, small size and low price, and is widely used in high-voltage pulse circuits. However, when a semiconductor switch is used to drive a pulse transformer, an over-voltage may be generated due to the influence of the leakage inductance, which not only increases the loss but also may lead to overvoltage breakdown of the switch. In this paper, the mechanism of overvoltage generation was analyzed, the effects and disadvantages of conventional overvoltage suppression methods were compared, a new overvoltage suppression circuit was proposed, and the topology structure, working principle and circuit parameter selection basis were given. The effects of the new over-voltage suppression circuit were verified through modeling and simulation. Finally, the overvoltage suppression circuit was used to develop a compact heavy-duty high-voltage pulse generator which can generate pulses with 11 kV amplitude, 2 kHz frequency, and 2 μs pulse width, drive a load of floating electrode dielectric barrier discharge and generate stable low temperature plasma.