The main objective of this study is to evaluate the antibacterial effect of antibacterial photodynamic therapy (aPDT) on Streptococcus mutans (S. mutans) biofilm model in vitro. The selection of photosensitizers is the key step for the efficacy of photodynamic therapy (PDT). However, no studies have been conducted in the oral field to compare the functional characteristics and application effects of PDT mediated by various photosensitizers. In this research, the antibacterial effect of Methylene blue (MB)/650 nm laser and Hematoporphyrin monomethyl ether (HMME)/532 nm laser on S. mutans biofilm was compared under different energy densities to provide experimental reference for the clinical application of the two PDT. The yield of lactic acid was analyzed by Colony forming unit (CFU) and spectrophotometry, and the complete biofilm activity was measured by Confocal Laser Scanning Microscopy (CLSM) to evaluate the bactericidal effect on each group. Based on the results of CFU, the bacterial colonies formed by 30.4 J/cm² 532 nm MB-aPDT group and 30.4 J/cm² 532 nm HMME-aPDT group were significantly less than those in other groups, and the bacterial colonies in HMME-aPDT group were less than those in HMME-aPDT group. Lactic acid production in all treatment groups except the photosensitizer group was statistically lower than that in the normal saline control group. The activity of bacterial plaque biofilm was significantly decreased in the two groups treated with 30.4 J/cm² aPDT. Therefore, aPDT suitable for energy measurement can kill S. mutans plaque biofilm, and MB-aPDT is better than HMME-aPDT.