[Objective] We studied the antibacterial effect of three Mongolian medicinal compounds against pathogenic Escherichia coli O1 and their protection of mice infected with E. coli O1. [Methods] The effects of Mongolian medicinal compounds on the growth curve, cell surface hydrophobicity, the cytoderm and cell membrane permeability of E. coli O1 were determined by turbidimetry, the microbial adhesion to solvents method, reagent kit and membrane permeability assay with ONPG as a substrate. In addition, the protection of mice was evaluated by E. coli O1 challenge. [Results] All three compound recipes inhibited the growth of pathogenic E. coli O1 and protected mice against E. coli O1. The highest protection rate (50%) was obtained for mice treated with Mongolian medicinal compound recipe III, as same rate as ciprofloxacin treated mice. When acting on the E. coli O1 cells, the decoction of Mongolian medicinal compound recipe III consisted of 7 herbs firstly changed the surface hydrophobicity of the cell and secondly destroyed the integrity of the cell wall over time, and then destroyed the cell membrane and changed the permeability, which eventually destroyed the cell structure. [Conclusion] Mongolian medicinal compound recipe III showed the best antibacterial effect against E. coli O1 both in vivo and in vitro and its protection rate in mice infected with E. coli O1 was comparable with the antibiotic ciprofloxacin.