In this study, genipin and glutaraldehyde in varied concentrations were utilized in chitosan crosslinking under alkaline condition. A UV/Vis analysis was used to investigate the molecular structure of genipin and glutaraldehyde in an aqueous alkaline solution. The results showed the formation of glutaraldehyde dimer and polymerized genipin. The FTIR-ATR, SEM, DSC, XRD, mechanical properties, crosslinking degree and swelling ratio of chitosan based films crosslinked by genipin and glutaraldehyde were determined. The results indicated that the hydrogen bonds formed between genipin and chitosan enabled the films crosslinked by genipin (1 and 5 mmol/L) to have a higher degree of crosslinking, but a lower swelling ratio than glutaraldehyde (1 and 5 mmol/L). Genipin enabled the chitosan-based film to possess better mechanical properties and crystallinity than glutaraldehyde. The polymerization of genipin had a substantial effect on the network structure and swelling behavior of chitosan-based films crosslinked by genipin.