The utilization of algicidal bacteria is becoming an attractive method for the inhibition of algae growth. However, the previous research has mainly focused on the control of harmful blooms in eutrophic waters by the addition of algicidal bacteria. This study aims to investigate the growth of algal cells in the presence of a sand-filter prevalent manganese-oxidizing bacterium, which might alleviate the algae-induced clogging problem in sand filters via bioaugmented sand filtration. The manganese-oxidizing bacterium Pseudomonas sp. QJX-1 exhibited an inhibiting effect on algae growth. Compared with a control group, the chlorophyll a content of M. aeruginosa could be significantly decreased by 60% after exposure to 10% QJX-1 culture supernatant. The decrease in photosynthetic parameters demonstrated the damage to the photosynthetic system of algal cells exposed to QJX-1 cell-free supernatant. The results indicated that QJX-1 inhibited the growth of M. aeruginosa by excreting an algicidal compound, 2,4-di-tert-butylphenol (2,4-DTBP), without directly contacting algal cells. The photosynthetic system structure of algal cells could be damaged through 2,4-DTBP excretion by QJX-1, which could explain the weakened photosynthetic activity of algal cells exposed to QJX-1. Our findings highlight the algicidal effect of the manganese-oxidizing bacterium Pseudomonas sp. QJX-1 on M. aeruginosa via the excretion of 2,4-DTBP.