The present invention relates to a system and a method for protecting a circuit between batteries, in which counter-electromotive force generated from the lead-storage battery is prevented from being applied to a MOSFET switch when power is cut off through the MOSFET switch in a circuit in which a vehicle lead-storage battery and a lithium polymer battery are connected to each other to prevent the MOSFET switch from overcurrent and prevent current, which leaks from the lead-storage battery when the lead-storage battery is charged, from being conducted to a path other than a determined path in advance.