The invention discloses a lightning arrester monitoring method applicable to an intelligent transformer station and a system. The method comprises the steps of (1) obtaining a leakage electric current original sample value of the lightning arrester, (2) performing re-sampling processing on the leakage electric current and SV voltage signals, (3) utilizing Fourier transform to calculate the leakage electric current and the amplitude and the phase of the re-sampling value of SV voltage signal, (4) calculating the included angle of the leakage electric current and the SV voltage signal according to the phase of the re-sampling value of the leakage current and the SV voltage signals, and calculating the resistance current according to a fundamental wave projection method, and (5) comparing the resistance current which is processed by median filtering with a set threshold value, and if the resistance current exceeds the preset threshold, performing in-place alarming. The system disclosed by the invention comprises a collection unit and a data processing unit. The method and the system reduce the electromagnetic interference and improve the fault detection accuracy o the lightening arrester.