Previously, we presented a novel approach for increasing Thermobifida fusca cutinase adsorption on cotton fibers by fusing cutinase with a carbohydrate-binding module (CBM). A preliminary study showed that two fusion proteins, namely cutinase-$CBM_{Cel6A}$ and cutinase-$CBM_{CenA}$, with similar stabilities and catalytic properties, had potential applications in bioscouring. In the present study, an indepth analysis of both cutinase-CBMs in bioscouring was explored. Effects of cutinase-CBMs on cotton bioscouring were investigated by characterizing the chemical and physical surface changes in enzyme-treated cotton fabrics. Gas chromatography/mass spectrometry was used to analyze the degradation of the cotton fabric cuticle; Fourier transform infrared microspectroscopy was used to study changes in the chemical composition of the cotton fabric epidermal layer; and scanning electron microscopy was used to monitor minor changes in the morphology of the fiber surface. Our results indicated that cutinase-CBMs in combination with pectinase had a greater effect on cotton fabric than did cutinase. Following scouring with cutinase-CBMs and pectinase, the performance of cotton fabric in terms of its wettability and dyeability was similar to that following alkali scouring. Our study provides a foundation for the further application of cutinase-CBM to bioscouring.