Objective: The antibacterial properties and bonding strength of 3M orthodontic adhesive resin modified by chlorhexidine acetate (CHA) composite mesoporous silica were investigated. Methods: CHA with different mass fractions was encapsulated in mesoporous silica nanoparticles (MSNs) (denoted CHA@MSNs). Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM) were used to characterize the samples. The 3M Z350XT flow resin was divided into 4 groups: group A: 3M+CHA@MSNs (0%); group B: 3M+CHA@MSNs (3%); group C: 3M+CHA@MSNs (5%); and group D: 3M+CHA@MSNs (6.4%), with mass scores of 0%, 3%, 5%, and 6.4%, respectively. The shear strength of the modified adhesive was tested by a universal electronic material testing machine, the adhesive residue was observed by a 10 × magnifying glass, and the adhesive Remnant index (ARI) was calculated. The four groups of modified adhesives were cultured with Streptococcus mutans. The OD540 value of the bacterial solution was measured by a spectrophotometer, and the amount of plaque attachment was observed by scanning electron microscopy to evaluate the antibacterial performance of the adhesives. Results: Infrared spectroscopic analysis of CHA@MSNs showed that CHA was successfully loaded onto MSNs. Under scanning electron microscopy, it could be seen that, after Cha was combined with MSNs, the structure of MSNs changed, as the boundary was fuzzy and aggregated into a layered structure. A comparison of shear strength revealed a statistically significant difference between the groups containing CHA@MSNs and the groups without CHA@MSNs (P<0.05). The value of the shear strength in group D decreased the most, while there was no statistically significant difference between group B and group C (P > 0.05). There was no statistical significance across all groups (P > 0.05), suggesting that the addition of CHA@MSNs had little effect on the bracket shedding. The OD540 value of bacterial fluid indicated that the difference among groups A, B and C was statistically significant (P < 0.05), and the antibacterial effect of group C was the best; there was no statistically significant difference between group C and group D (P > 0.05). Conclusions Therefore, adding 5% CHA@MSN antibacterial agent significantly improved the antibacterial effect and did not affect the bond strength.