Abstract: For studying the effects of pectinase treatment on structures and fiber properties of naturally colored cotton fiber,the moisture absorption,fiber strength,chromatism and waxy materials content of the treated samples were tested.Surface structure and pigment distribution of the samples before and after treatment were observed by scanning electron microscope and bio-microscope respectively,and compared with those by alkali treatment,The results showed that pectinase treatment is beneficial to environmental protection of naturally colored cotton,improves its moisture absorption significantly without noticeable adverse effect on the fiber strength and structure,or the contents of waxy substance and pigments.So pectinase treatment is more suitable for improving the moisture absorption of naturally colored cotton.