Abstract：In Shennong Bencao Jing，there are 89 Chinese medicines that can treat pathogens. Through the analysis on category distribution， nature of medicine and modern application of there Chinese medicines， it is found that they can be classified into three grades，namely the top grade，the medium grade and the low grade，and the most common nature of medicine is bitter-cold，followed by bitter-neutral，sweet-neutral，and pungent-warm. It is suggested that there are two ways of treating pathogens by these medicines，the direct elimination of pathogens and an indirect way of tonifying qi and blood or warming yang to resolve dampness. Among 89 Chinese medicines，42 are still used to treat pathogens，involving 16 efficacy classifications of modern Chinese medicine，mainly including deficiency-supplementing medicine，heat-clearing medicine ， exterior- releasing medicine ， phlegm- resolving medicine ， and astringent medicine. The complicated action mechanism of medicine for the treatment of pathogens in Shennong Bencao Jing should be further studied and analyzed in combination with clinical experience.