Objective To investigate the effect and molecular mechanism of botulinum neurotoxin serotype A (BoNT/ A) heavy chain on neuron regeneration. Methods Cell culture, rats, immunofluorescence, SDS?PAGE and western blot, etc. were adopted in this study to explore the alterations of histone?3 acetylation (acetyl?H3) by local treatment of BoNT/ A heavy chain to spinal cord injury (SCI) in rats (in vivo) or by adding it into cell culture (in vitro). Meanwhile, the relevance of acetyl?H3 to neurite out?growth based on SCI and cell culture with BoNT/ A heavy chain application was approached as well. Results The application of BoNT/ A heavy chain to cultured Neuro?2a cells increased the level of H3 acetylation. The increase of H3 acetylation was paralleled with the growth of neuritogenesis. Also, the neuronal treatment of BoNT/ A heavy chain to SCI promoted the re?growth of neuronal processes surrounding the lesions. The growth of neuronal processes was positively correlated to the level of H3 acetylation. During the periods of BoNT/ A heavy chain treatment in vivo or in vitro, the increase of H3 acetylation showed two peaks. Conclusions BoNT/ A heavy chain increased the H3 acetylation, which might be one of its neuritogenic mechanisms.