Botryosphaeria trunk canker is arguably the most damaging disease of Carya cathayensis (Chinese hickory) in China. Fungicides are commonly applied to control the disease but have serious environmental issues. Here, the Gram‐positive bacterium Paenibacillus polymyxa strain CF05 was evaluated as an alternative for the preventive control of Botryosphaeria trunk canker on C. cathayensis. In vitro, this strain was inhibitory to the growth of B. dothidea, a causal agent of Chinese hickory trunk canker. Formulation of strain CF05 endospores in a carboxymethylcellulose/poly (vinyl alcohol) (CMC/PVA) blend showed high stability over a 12‐month period. A two‐year field experiment suggested that the CMC/PVA formulated strain CF05 reduced the occurrences of both new cankers and established cankers, displaying an efficacy comparable to treatment with thiophanate‐methyl. Furthermore, strain CF05 greatly induced production of phenylalanine ammonia lyase (PAL), polyphenol oxidase (PPO) and peroxidase (POX) by C. cathayensis seedlings, which showed maximum activity of these enzymes 2 days postinoculation (dpi) and increased phenol contents inside the trunk throughout the experimental assessment period. In summary, the P. polymyxa strain CF05 CMC/PVA formulation has promise as a potent environmentally friendly agent for the preventive biocontrol of C. cathayensis trunk canker.