This study examined the relationships between protein expression and Poly ADP ribose polymerase in brain cell death in brains damaged by thrombotic stroke and treated with the Full Wave- Cockroft Walton (FWCW) method of Transcranial Magnetic Stimulation (TMS). The two-way switching element for TMS drove a halfbridge inverter of the current resonance of direct current voltage (+) and direct current voltage (−), and the experiment was conducted by stimulating the mice with thrombotic stroke through a range of pulses. Thrombotic stroke was caused of ligation of the common carotid artery of male SD mice, and blood reperfusion was conducted five minutes later. Protein expression was examined in immune reaction cells, which reacted to an antibody to Poly ADP ribose polymerase in the cerebrum cells, and western blotting. Observations of the PARP changes after thrombotic stroke showed that the number of Poly ADP ribose polymerase reactions were significantly lower (p < 0.05) in the group treated with TMS of the FWCW than the group with thrombotic stroke 24 hours after its onset. The application of FWCW-TMS helped prevent the necrosis of nerve cells and might prevent the brain damage that occurs as a result of thrombotic stroke, and improve the function recovery and disorder of brain cells.