Objective To analyse the characteristic electrophysiological changes of anisometropic and strabismic amblyopia, and explore the pathogenic mechanisms of the two kinds of amblyopia. Methods The visual evoked potential (VEP) and contrast sensitivity (CS) examinations were performed on 20 anisometropic amblyopic, 9 strabismic amblyopic and 18 non-amblyopic children by RETI scan 3.15 system of Roland. The latencies, amplitudes and CS were analysed and compared among amblyopic eyes, fellow eyes and non-amblyopic eyes. Results The latency of anisometropic amblyopia was prolonged in high spatial frequency and the latency of strabismic amblyopia was prolonged in whole spatial frequency. The amplitudes of the two kinds of amblyopia decreased in low spatial frequency. There was no difference between the fellow eyes of anisometropic amblyopia and non-amblyopic eyes. The latency of the strabismic amblyopic fellow eyes was significantly longer than that of the non-amblyopic eyes in low spatial frequency (P < 0.05). The CS of both amblyopic and fellow eyes of anisometropic amblyopia was not different from that of the non-amblyopic eyes. The CS of the strabismic amblyopic eyes was lower than that of the nonamblyopic eyes in whole spatial frequency (P < 0.05), but their fellow eyes were better (P < 0.05). Conclusions The study results support that anisometropic amblyopia and strabismic amblyopia have different neural mechanisms, and the fellow eyes of strabismic amblyopia could not be looked as 'healthy eyes'. The VEP and CS examinations have significant clinical value in the diagnosis of amblyopia.