The invention discloses high resistance grounding detection system, device and method for a small current grounding system. The system comprises a grounding wire selecting device, a flexible voltage source and a boosting transformer, wherein the grounding wire selecting device is connected with the flexible voltage source, a high voltage side of the boosting transformer is connected between a neutral point of the system and the ground, and a low voltage side of the boosting transformer is connected with the flexible voltage source; and the flexible voltage source is used for receiving commandsissued by the grounding wire selecting device and emitting an appointed voltage vector to the low voltage side of the boosting transformer. The method comprises the following steps: when a groundingfault does not occur, injecting a non-power frequency voltage through the neutral point, collecting a bus zero sequence voltage and a zero sequence current of each branched circuit, and calculating the zero sequence capacitive reactance of each branched circuit; and when a grounding fault occurs, calculating power integration and a resistance value of a grounding point according to the zero sequence capacitive reactance of each branched circuit, a collected bus three-phase voltage, the zero sequence voltage and the zero sequence current of each branched circuit, and selecting a grounding wire.The invention further discloses a corresponding high resistance grounding detection device. According to the system, the device and the method, the high resistance grounding recognition capacity of the small current grounding system is improved.