Microbial pollution commonly causes serious pipe corrosion in oil-field reinjection water systems. As an alternative and environmentally friendly inactivation technology, the pulsed electric field (PEF) process is employed to inactivate microorganisms in oil-field reinjection water. The effects on inactivation of process parameters including electric field strength, process temperature, initial bacteria concentration, and conductivity were investigated. The results showed that electric field intensity is the most important parameter in PEF inactivation. After a 20-min treatment, the inactivation efficiency was a 2.8 log reduction for saprophytic bacteria, a 3.6 log reduction for iron bacteria, and a 3.9 log reduction for sulfate-reducing bacteria. Transmission electron microscopy observations of the bacteria confirmed that PEF technology can lead to severe surface damage and rupture to the cells. Moreover, a possible mechanism of inactivation is discussed and used to explain the influence of process parameters on PEF treatment.