The present disclosure directs to a system and method for configuring a pulse sequence in MRI. The method may include obtaining a preliminary gradient pulse configuration, wherein the preliminary gradient pulse configuration relates to a portion of a pulse sequence to be implemented by one or more coils of an MR scanner, the pulse sequence including a plurality of gradient pulses. The method may also include determining a global peripheral nerve stimulation (PNS) value of the preliminary gradient pulse configuration according to a PNS model. The method may further include determining a target gradient pulse configuration based at least in part on the preliminary gradient pulse configuration, the global PNS value, and a PNS threshold.