The invention discloses an energy-pumped reactor protection method and system based on the principles of phase comparison and amplitude comparison. By judging whether the calculated zero sequence current of the main reactance winding, the zero-sequence current of the pumping winding side, the zero-sequence current abrupt change of the main reactance winding, the zero-sequence current abrupt changeof the pumping winding side and the current change coefficient satisfy the phase comparison criterion or arbitrary amplitude comparison criterion, and whether the differential threshold criterion issatisfied, whether the pumping reactor protection operates or not is determined; if so, the pumping reactor protection operates; otherwise, the pumped reactor protection does not operate. The invention improves the reliability of the protection of the energy-pumping reactor. The protection of the pumped reactor does not need voltage, and it can operate reliably when the PT line is broken. The pumped reactor protection can protect the main reactance winding inter-turn fault, the pumped winding inter-turn fault and all other faults with zero sequence current at the same time, which avoids the redundant configuration of protection. The pumped reactor has high protection sensitivity and can identify slight turn-to-turn faults.