Recently, electrospinning of nanofibers based on chitosan has been widely studied and numerous chitosan based nanofibers have been prepared, for the enormous possibilities of applications in various areas such as filtration, enzyme immobilization, tissue engineering, wound dressing, drug delivery, and catalysis. Because most of the chitosan based nanofibers are soluble in aqueous solutions and the other properties such as mechanical properties are not suitable for the further applications. It is necessary to improve the properties of chitosan based nanofibers. Various post-processing has been done to the chitosan based nanofibers and many post-processing products have emerged. This article discusses the post-processing of the chitosan based nanofibers involving methods, mechanisms, changes of nanofiber properties, and applications of the post-processing products in details. The post-processing is divided into alkali treatment, crosslinking, and functionalizing.