In this paper the effect of cutinase on the degradation of cotton seed coat is analyzed. Fourier transform infrared (FT-IR) microspectroscopy was applied to study the changes of chemical compositions in cotton seed coat epidermal layer and gas chromatography/mass spectrometry (GC/MS) was used to analyse cutinase depolymerization of cotton seed coat. Based on these arguments the ability of cutinase to degrade aliphatic components in cotton seed coat was verified. Positive effect of cutinase on degradation of cotton seed coat was observed with the combination of alkaline pectinase or xylanase. The removal of aliphatic components by cutinase enables other enzymes to penetrate into the inner of cotton seed coat. Cutinase can potentially improve the degradation of cotton seed coat during cotton fabric bio-scouring process.