The invention relates to a bioherbicide composition and application thereof and belongs to the field of agricultural chemicals. The bioherbicide composition is missible oil, wettable powder, emulsion in water and water dispersible granules prepared from active ingredients including nonanoic acid and acetic acid, minor ingredients including a solvent, a carrier and a surfactant as well as other additives. By weight, the active ingredients account for 10-97% of the bioherbicide composition, the surfactant accounts for 1-8% of the bioherbicide composition, and the carrier and the other additives account for 2-80% of the bioherbicide composition. The bioherbicide composition can be used for directed spraying of urban courtyards and crop fields to control and kill gramineae, cyperaceae and broadleaf weeds and is wide in weeding spectrum, quick to act, high in control efficiency, safe and the like.