Novel amphipathic derivative of chitosan (carboxymethyl-hexanoyl chitosan, CHC) was made into mats of nanofibers (similar to 100 nm) via electrospinning. The resulting mats were further cross-linked with genipin. The morphology of CHC nanofibers was examined using a field emission scanning electron microscope (FESEM). The optimum parameters of CHC nanofiber was achieved when the CHC concentration was 4 wt% and electrospinning was conducted with a voltage of 20 kV over a distance of 10 cm. The characterizations of biocompatibility, hemocompatibility, and anti-bacterial activity of the nanofibers were also investigated. The results show that CHC nanofibers still preserved anti-bacterial activity and thrombogeneicity owing to those residual amino groups of chitosan and exhibit high biocompatibility for L929 fibroblast test. Thus CHC exhibited the potential to serve as a novel wound dressing and surgical implants application by these advanced features.