The secondary metabolites, phenazine products, produced by Pseudomonas aeruginosa can mediate the electrons transfer in microbial fuel cells (MFCs). How increase the total electricity production in MFCs by improving the characteristics of Pseudomonas aeruginosa is one of research hot spots and problems. In this study, P. aeruginosa strain SJTD-1 and its knockout mutant strain SJTD-1 (ΔmvaT) were used to construct MFCs, and the discharge processes of the two MFCs were analyzed to determine the key factors to electricity yields. Results indicated that not only phenazine but also the viable cells in the fermentation broth were essential for the discharge of MFCs. The mutant strain SJTD-1 (ΔmvaT) could produce more phenazine products and continue discharging over 160 hours in MFCs, more than that of the wild-type SJTD-1 strain (90 hours discharging time). The total electricity generated by SJTD-1 (ΔmvaT) strain could achieve 2.32 J in the fermentation process, much higher than the total 1.30 J electricity of the wild-type SJTD-1 strain. Further cell growth analysis showed that the mutant strain SJTD-1 (ΔmvaT) could keep a longer stationary period, survive much longer in MFCs and therefore, discharge more electron than those of the wild-type SJTD-1 strain. Therefore, the cell survival elongation of P. aeruginosa in MFCs could enhance its discharging time and improve the overall energy yield. This work could give a clue to improve the characteristics of MFCs using genetic engineering strain, and could promote related application studies on MFCs.