Dental resin composites (DRCs) are commonly used to restore teeth affected by dental caries or defects. These materials must possess excellent properties to withstand the complex oral environment. The objective of this study was to prepare and characterize Boron nitride nanosheets (BNN)/ dimethyl amino hexadecyl methacrylate (DMAHDM) composites (BNN/DMA), and to evaluate them as functional fillers to enhance the mechanical and antimicrobial properties of dental resins. The BNN/DMA composites were successfully prepared under the theoretical guidance of molecular dynamics (MD), and then the physicochemical and morphological characterization of the BNN/DMA composites were carried out by using various test methods, such as FT-IR, XRD, UV−vis spectroscopy, SEM, TEM, and AFM. It was doped into the dental flowable resin in a certain proportion, and the results showed that the flexural strength (FS), elastic modulus (EM), compressive strength (CS), and microhardness (MH) of the modified resin composites were increased by 53.29, 47.8, 97.59, and 37.1%, respectively, with the addition of 0.8 wt % of BNN/DMA composite fillers. It has a good inhibition effect on Streptococcus mutans, with an inhibition rate as high as 90.43%. Furthermore, this effect persists even after one month of aging. In conclusion, the modification of flowable resins with low-concentration BNN/DMA composites favorably integrates the mechanical properties and long-term antimicrobial activity of dental resins. At the same time, they have good biocompatibility and do not affect the aesthetics. The BNN/DMA composite modified flowable resin has the potential to become a new type of antimicrobial dental restorative material.