Based on membrane electro-dialysis system, a novel hydrogen autotrophic MBBR (Moving Bed Biological Reactor) was established to remove perchlorate from aqueous solution. In cathode chamber, bacteria could utilize hydrogen as electron donor to transform perchlorate to chloride ion; in anode chamber, the chloride ion was oxidized to active chlorine to improve effluent quality. The conversion of perchlorate and the influential factors were explored. The hydraulic retention time (HRT) was maintained at 4h. For 4.98±0.091mg/L ClO₄^- in feed water, when current intensity increased from 6to 15mA, the removal efficiency increased from (39.75±2.09)% to (98.99±0.05)% correspondingly. The active chlorine increased from 0.057±0.003 to 0.070±0.0002mg/L. The pH of effluent was kept at 7.96~8.11 and the turbidity was 0.89±0.27NTU. When further increase current intensity to 20mA, the pH of cathode chamber exceeded 9.5 thus inhibiting the activity of microorganism and the removal efficiency decreased sharply to (30.75±1.19)%. Besides, scanning electron microscope (SEM) was used to analyze the morphology of bacteria. The dominant bacterial was mainly short rod-shaped, attached to the surface of carriers and proliferated slowly. High-throughput sequencing was applied to analyze bacterial samples after inoculation and 24d operation. The results indicated that the α-biodiversity was decreased during the operation time and the Thauera was the dominated bacteria with 8.25% abundance.