The invention discloses a leakage current compensation system of a lightning arrester in a power site environment. The system comprises a current sensor, an operational amplifier, a current output unit and a DC inhibition unit; the current sensor is connected to a grounding current measuring loop of the lightning arrester in the power site environment and used to measure the power-frequency and harmonic leakage currents of the lightning arrester; the operational amplifier amplifies an output current of the current sensor in real time; the current output unit converts an output voltage of the operational amplifier into a current via a fourth resistor, and outputs the current to the current sensor; and the DC inhibition unit is connected with the operational amplifier in parallel, and used to inhibit a DC output component of the operational amplifier. The system and method have the advantages that the output current of the lightning arrester is measured, and the compensation current whose magnitude is the same with the magnitude of the output current and phase is opposite to the phase of the output current is input in real time, so that the working flux of the current measuring loop of a sample approaches 0, and the background leakage current of the lightning arrester is prevented from interfering in verification.