The invention relates to an antibacterial paper towel and a preparation method thereof, and discloses a process for papermaking by using Qianjinfang medicine residue, wherein the process comprises: microwave pretreatment, fermentation, washing, paper making, extracting of medicinal ingredients from waste liquid, paper modification and the like. According to the present invention, the short fiber is prepared by using the Qianjinfang medicine residue, and the long fiber property of the cotton fiber is combined, such that the prepared antibacterial paper towel has good tensile property; the prepared antibacterial paper towel has remarkable wet strength through internal sizing and surface application; by using the microwave radiation method and the biological method, harmful chemicals are notintroduced during the whole process, such that the hygienic characteristics of the paper are ensured; and the medicinal ingredients are extracted from the pulping waste liquid, and are mixed with thebase medicine liquid component comprising Cortex Ailanthi, Sophora flavescens Ait, Cortex Moutan, frankincense and borneol, and the obtained mixture is applied on the paper, such that the obtained antibacterial paper towel has good anti-inflammatory and antibacterial effects, can prevent microbial infection, does not have irritation and side effects on the skin and vaginal mucosa, and is suitablefor women.