To study the effects of soil microbes of habitats on the cuttings rooting of Huperzia serrata and its mechanism.The cuttings of H. serrata were planted on the primary habitat soil and on the soil autoclaved, rooting rates were examined respectively. Changes of contents of phenolic compounds (catechin, quercetin, chlorogenic acid, ferulic acid) and indoleacetic acid (IAA) , and changes of activities of polyphenoloxidase (PPO) and peroxydase (POD) during the cuttings rooting were determined.Soil microbes of primary habitat could increase the rooting rate and the number of roots, could increase contents of catechin, chlorogenic acid, ferulic acid and IAA during rooting, and could affect activities of PPO and POD.During the rooting higher contents of catechin, chlorogenic, ferulic acid and IAA caused by soil microbes of primary habitat are important factor for rooting rate.