Genipin (GP) as a natural crosslinker has gained much attention in the food industry on account of its high biocompatibility and safety. In this paper, chitosan (CS)‐soy protein isolate (SPI) crosslinked films were prepared using GP as a crosslinking agent. Crosslinking reaction with high contents of GP (0.03%, 0.05%) changed the rheological property of the film matrixes. The crosslinking degree was positively correlated with the content of GP, which was from 21.08 ± 3.95% of CS‐SPI‐1 to 39.66 ± 1.62% of CS‐SPI‐5. Fourier transform infrared spectroscopy spectra confirmed the crosslinking reaction. The X‐ray diffraction and scanning electron microscopy analyses indicated that the crosslinking reaction decreased the crystallinity degree and enhanced the surface roughness of CS‐SPI film, respectively. The crosslinking reaction did not significantly affect the thickness, moisture content and water solubility of CS‐SPI film. Crosslinked films presented better light barrier capacity. The tensile strength (TS) of CS‐SPI‐1 was increased by 50%, however, further increasing the contents of GP (0.03%, 0.05%) reduced the TS of the crosslinked films. With the increasing incorporation with GP, the EAB was significantly decreased, while the modulus increased from 95.76 ± 25.78 to 508.78 ± 77.95 MPa. The crosslinking reaction improved the rigidity of CS‐SPI film. Low crosslinking degree could improve thermal stability of CS‐SPI, while higher GP addition (0.03%, 0.05%) decreased the thermal stability and prolonged the degradation time of the film in soil. The results indicated that low crosslinking reaction could improve the property of CS‐SPI film, enhancing its potential application in food packaging.