The invention provides a method for scouring a cotton fabric by applying cutinase and CBD (cellulose-binding domain)-alkaline pectinase, belonging to the technical field of treatment of cotton fabrics before dyeing and finishing. The method comprises the following steps of: treating a cotton knitted fabric, cotton yarns, or a cotton woven fabric from which size is removed by amylase or sodium hydroxide firstly, in a mixed enzyme solution formed by cutinase and CBD-alkaline pectinase; or respectively treating in the cutinase solution and the CBD-pectinase solution, wherein the hydrophobic surface structure of cotton fibers is destructed by the cutinase, the higher fatty acid ester substances are removed from the surface waxy layers of the cotton fibers, so that the wettability of the cotton fabric is improved, the pectic substances on the cotton fibers are exposed, and then the CBD-pectinase is absorbed on the surface cellulose of the cotton fibers to decompose the pectic substances on the cotton fibers. By the method provided by the invention, on the one hand, the traditional chemical treatment method can be substituted for scouring the cotton fabric, and on the other hand, because the cutinase and the CBD-alkaline pectinase are adopted, the wettability of the cotton fibers and the pectin removal rate are improved.