The invention discloses an intelligent pulse cut-off system which comprises a signal detection isolation module, a signal processing module and a pulse control module that are connected successively. The signal detection isolation module is used for detecting an opening signal of a magnetic blow-out switch; the signal processing module receives the opening signal and sends out a pulse cut-off instruction based on a processing logic; and the pulse control module receives the pulse cut-off instruction and carries out pulse cutting off. In addition, the invention also discloses a method of the system. Compared with the prior art, the intelligent pulse cut-off system and method thereof have the following advantages: the reliability of deexcitation of the excitation system is improved; the operation becomes simple and safe; a solution of deexcitation of a jumper is provided for a high-capacity generator set; and a risk of a deexcitation accident of the generator set due to a deexcitation loop fault is reduced to the greatest extent.