Along with the current increases in human activities, air pollution, especially that generated from bioaerosols, has begun to receive more extensive attention. Among the bioaerosols, bacteria and fungi can result in organisms that are pathogenic to animals and humans. Therefore, a biological protective respirator with an antibacterial function would be a significant method by which to prevent epidemic spread of respiratory infectious diseases and protect human health. In this study, a type of facemask with an antibacterial function was prepared. The structure of the respirator included a respirator body and an inner filter layer that was assembled with herbal microcapsules. A kind of Chinese herb microcapsule developed through a cross-linking reaction method was successfully prepared to serve as an important component of the respirator. Scutellaria baicalensis (SB), a typical Chinese medicine, was employed to prepare the Chinese herb microcapsule. Three kinds of filter cloth (cotton, polyester fiber, and non-woven fabric, respectively) were employed to assemble with Chinese herb microcapsule. Meanwhile, the antibacterial performance and adhesion of the Chinese herb microcapsule for E. coli and S. aureus were investigated. The measurement results revealed that (i) the antibacterial efficiency of the Chinese herb microcapsule and the respirator filter was above approximately 99.999 and 96.000%, respectively; (ii) the adhesion of the herb microcapsules was still excellent after the filter was washed 100 times; (iii) the as-prepared antibacterial filter modified by an O2 plasma-surface (PSM-O2) treatment exhibited excellent antibacterial performance. Finally, a chamber simulation utilizing an Anderson first order sampler was designed to simulate the effect of wearing the antibacterial filter in a real environment. Overall, the respirator exhibited excellent biological protection properties compared with general masks, which will satisfy a vast number of application prospects.