Recently, increasing attention has been paid to natural polysaccharides for their low cost, biocompatibility and biodegradability. Quaternization is a modification method to improve the solubility and antibacterial ability of natural polysaccharides. Water-soluble derivatives of cellulose, chitin and chitosan offer the prospect of diverse applications in a wide range of fields, such as antibacterial products, drug delivery, wound healing, sewage treatment and ion exchange membranes. By combining the inherent properties of cellulose, chitin and chitosan with the inherent properties of the quaternary ammonium groups, new products with multiple functions and properties can be obtained. In this review, we summarized the research progress in the applications of quaternized cellulose, chitin and chitosan in recent five years. Moreover, ubiquitous challenges and personal perspectives on the further development of this promising field are also discussed.