A method for microbial fermentation of botanicals includes steps of: fermenting with wall-breaking fungi, and then fermenting with probiotics. The wall-breaking fungi are wood-grown fungi and/or Cordyceps. The method can effectively destroy the cell wall of the botanical, promote release of effective ingredients of the botanical and improve utilization rate of the botanical. In addition, due to fermenting with the wall-breaking fungi, the botanical medicine also contains the active ingredients of the wall-breaking fungi. Thereby the efficacy of the botanical is increased.