In order to improve the stability of waterborne polyurethane fixative during the color-fixing treatment, a novel environment-friendly cationic waterborne polyurethane (CWPU) containing quaternary ammonium groups was synthesized from isophorone diisocyanate, polypropylene glycol, butanone oxime, and N-methyl dihydroxyethyl allyl ammonium chloride (MDAAC) and dispersed in water by using diethylenetriamine as the post-chain extender. The structures of the MDAAC and CWPU were characterized by 1H-NMR and FTIR. Effects of R-value, MDAAC content, post-chain extender and blocking agent on the properties of the waterborne polyurethane emulsion and the rubbing fastness of the treated dyed cotton fabrics were investigated. The investigation results showed that the R-value and the cationic group content of the cationic waterborne polyurethane had no significant effect on the color-fixing performance, but the content of DETA had a great influence on the wet-rubbing fastness. The wet rubbing fastness of the treated cotton fabrics was promoted from grade 1–2 to grade 3. Furthermore, the quaternary ammonium groups were able to provide the surface charges for the stabilization of the resulting polymer in alkaline electrolyte solution which met the requirements of practical applications.