To investigate the degradation effect of bovine trypsin on multispecies biofilm of caries-related bacteria and provide an experimental foundation for the prevention of dental caries. Standard strains of S. mutans, S. sanguis, S. gordonii, and L. acidophilus were co-cultured to form 24h, 48h, and 72h biofilms. The experimental groups were treated with bovine trypsin for 30s, 1min, and 3min. Morphological observation and quantitative analysis of extracellular polymeric substances (EPS), live bacteria, and dead bacteria were conducted using the confocal laser scanning microscope (CLSM). The morphological changes of EPS and bacteria were also observed using a scanning electron microscope (SEM). When biofilm was treated for 1 min, the minimal inhibitory concentration (MIC) of bovine trypsin to reduce EPS was 0.5mg/mL in 24h and 48h biofilms, and the MIC of bovine trypsin was 2.5mg/mL in 72h biofilms (P < 0.05). When biofilm was treated for 3min, the MIC of bovine trypsin to reduce EPS was 0.25mg/mL in 24h and 48h biofilms, the MIC of bovine trypsin was 1mg/mL in 72h biofilm (P < 0.05). The ratio of live-to-dead bacteria in the treatment group was significantly lower than blank group in 24h, 48h, and 72h multispecies biofilms (P < 0.05). Bovine trypsin can destroy multispecies biofilm structure, disperse biofilm and bacteria flora, and reduce the EPS and bacterial biomass in vitro, which are positively correlated with the application time and concentration.