Many studies have reported that a certain preference is obeyed by perchlorate-degrading bacteria to utilize different electron acceptors. This conclusion was stated considering only the removal rate of different electron acceptors, indicating a lack of adequate proof. This study investigated the selective utilization of different electron acceptors by a perchlorate-degrading bacterium. The results showed that the mixed population of microorganisms (containing perchlorate-degrading bacteria) obeyed a certain sequence to utilize different electron acceptors, which was oxygen > nitrate > perchlorate > sulfate. The results of high-throughput sequencing showed that the mixed population of microorganisms contained anaerobic bacteria, facultative anaerobic bacteria, and aerobic bacteria. The microbial community structure actually had been changed by adding another electron acceptor to the perchlorate-medium and the microbial genera were distinguished in terms of utilizing the specific electron acceptor (e.g., oxygen, nitrate, sulfate). The result of canonical correspondence analysis demonstrated that the abundance of microorganisms appeared as a good positive correlation with the corresponding electron acceptor. Therefore, a new viewpoint was inferred that there are two main reasons at least that make the mixed microorganisms obey a certain sequence to utilize different electron acceptors. One reason is that the perchlorate-degrading bacteria in the mixed microorganisms change their own respiratory metabolism pathway. The other reason is that the mixed microorganisms actually change their microbial community structure.