The invention discloses a trichoderma atroviride strain and application thereof to tobacco. The strain is a trichoderma atroviride C9-13 strain, and the preservation number is CGMCC No.8077. The strain can degrade pectin and cellulose at the same time. A method for applying the trichoderma atroviride C9-13 strain to treating the tobacco comprises the steps that trichoderma atroviride C9-13 is firstly taken to be cultured, then a spore suspension is prepared, then the spore suspension is added to a fermentation medium to be cultured, fermented supernatant fluid is prepared, and finally the fermented supernatant fluid is sprayed to the surface of the tobacco. The content of pectin and cellulose of the treated tobacco is obviously reduced, smoking quality, especially the fragrance amount is improved to a certain degree, and the chemical ingredient harmony is also improved.