[Objective] The study aims to elucidate the effects of three exogenous substances on the root rot disease of continuously cropped Codonopsis and their impact on its physiological and biochemical properties, providing a reference for the use of these substances to alleviate the root rot disease associated with continuous cropping of Codonopsis. [Methods] Using one-year-old potted Codonopsis seedlings as experimental materials, we established a blank control, a pathogen infection treatment, and subsequent treatments with 28-homomethionine for root drenching, foliar spray, Bacillus subtilis, Bacillus amyloliquefaciens, and amino acid water-soluble fertilizer after infection. We investigated the inhibitory rate of the root rot disease in continuously cropped C. pilosula and the changes in its physiological and biochemical properties. [Results] The biocontrol bacteria B. subtilis and B. amyloliquefaciens can significantly inhibit the growth of pathogenic fungi infecting C. pilosula, with an inhibition rate of over 70%. The application of 28-homolinolenic acid through root drenching, foliar spray, and amino acid water-soluble fertilizer significantly increases chlorophyll content, enhances the activity of antioxidant enzymes such as SOD, POD and CAT, and markedly reduces cellular membrane damage and the extent of lipid peroxidation. Additionally, biocontrol treatments significantly decrease the accumulation of soluble sugars, MDA, proline and soluble proteins, restoring them to normal levels. [Conclusion] Biocontrol agents such as B. subtilis can effectively inhibit the growth of pathogenic fungal hyphae and the germination of spores. Plant growth regulators and amino acid water-soluble fertilizers can balance the osmotic adjustment system, enhance the antioxidant defense mechanism, promote photosynthesis, and strengthen the plant"s stress resistance.