The potential of nine fungal strains for pre-treating Eucommia ulmoides Oliver seed shells (EUOSSs) was investigated. Phanerochaete chrysosporium Burds. was found to be the best fungal strain for pre-treating EUOSSs. After co-pre-treatment with acetic acid and P. chrysosporium Burds., which was cultivated in a solid state with an approximately 74% moisture content at 28 °C for 28 d, the weight loss of the EUOSSs was 51.9%. Because of the cooperative efficiency of the biochemical pre-treatment, an enzymatic digestibility value of 86.6% was achieved. The high digestibility value was attributed to the synergism between the acetic acid and fungal treatments, which led to improved enzymatic accessibility of the EUOSSs. As an environmentally friendly processing method, fungal pre-treatment can save a great amount of energy and, in combination with an acetic acid treatment, is more efficient at improving the rate of sugar transformation.