The invention discloses a cotton and polyester cotton blended fabric pre-treatment method. The method comprises the following steps: blank cloth preparing, composite biological enzyme pre-treatment, piling, washing, drying, dip padding on ginned cotton enzyme, steaming, washing and drying. According to the invention, lignin, starch slurry, cotton wax and cottonseed hull on the fabrics are degraded and emulsified by using a compound enzyme system, cooperation usage of lignin enzyme and cellulase is helpful for removing lignin of cottonseed hull and fiber cell wall, the composite pectase is introduced into a primary cell wall layer so that the pectic substances are degraded, a channel to a fiber cyst cavity is opened, staple fiber on the surface of yarn beam is removed by cellulose, the problem of difficult removal of the cottonseed hull during bio-enzyme treatment is effectively solved, caustic soda, a chemical agent, steam, electric power, water volume and COD content of sewage are reduced, a production process is simple and controllable, the processing of the multi-fiber composite fabrics is simple and easy, and quality of the product is increased.