There is an increasing demand for crosslinking methods of silk fibroin (SF) scaffolds in biomedical applications that could maintain the biocompatibility, bioactivity as well as improve the water resistance and mechanical properties of SF materials. In this study, SF was crosslinked effectively with genipin which is a naturally occurring iridoid glucoside and the crosslinking mechanism was investigated through FTIR and amino acid analysis. The results showed that genipin could react with the -NH₂ groups on the side chains of SF macromolecules and to form inter- and intra-molecular covalent bonds, and improved the stability of SF materials significantly. In vitro, the performances of genipin-crosslinked SF films were assessed by seeding L929 cells and compared with ethanol-processed SF films, glutaraldehyde and polyethylene glycol diglycidyl ether crosslinked ones. The genipin-crosslinked SF films showed a similar affinity to cells as ethanol-processed ones, and a higher bioactivity in promoting cell growth and proliferation, inhibition of cell apoptosis, and maintenance of normal cell cycle compared with glutaraldehyde and polyethylene glycol diglycidyl ether crosslinked SF films. These features, combined with the decrease of brittleness of SF films crosslinked with chemical methods, substantiated genipin as an effective and biocompatible agent for the manufacturing of bioactive SF materials which used as tissue engineering scaffolds and drug delivery carriers.