This study explored the effect of a pulsed electric field (PEF) on the anaerobic ammonium oxidation (ANAMMOX) process at room temperature (20 +/- 1 degrees C). The influences of different modes of PEF (R1), a direct current electric field (R2) and a control reactor (R3) were determined through long-term tests. The results showed that R1 shortened the start-up time and led to excellent nitrogen removal. At this stage, the activities of key enzymes of R1 were much higher than those of R3. The high-throughput sequencing results showed that the relative abundance of functional bacteria in R1 was higher than that in R2 and R3. The mechanism by which the PEF enhanced ANAMMOX might be the improvement of the speed of ion and molecular migration that occurred by changing the permeability of the cell membrane under the PEF.