Polysaccharide-protein conjugations have generated increasing interests for biomedical applications in recent years. A naturally occurring cross-linking reagent, genipin, which has been used in herbal medicine, was employed to cross-link chitosan and gelatin for the preparation of a novel chitosan-gelatin conjugate. The primary amine groups on chitosan and gelatin were covalently linked with genipin, leading to the formation of a chitosan-gelatin conjugate with nitrogen-containing heterocycle units, the pyrindine-like derivatives. The FT-IR and UV-vis studies revealed that chitosan could react with genipin via a nucleophilic ring-opening reaction to construct more sufficient and extensive cross-link networks, as compared with its gelatin counterpart. The UV-vis absorption properties of the chitosan-gelatin conjugates were strongly related to the chitosan-to-gelatin weight ratio in the compositions. It is worth noting that the conjugation process endows the special emission properties of the chitosan-gelatin conjugates, which depends on the cross-linking reaction and the formation of hydrogen bonding involved chitosan-gelatin complex. Fluorescence quenching or enhancement was observed from the chitosan-gelatin conjugates upon coordinated with a wide variety of heavy metal ions (Ag+, Cu2+, Fe2+, and Co2+). This study also examined the possibility of covalent coupling the capture chelator (chitosan) with bioactive protein (e.g., albumin, alpha-globulin, and fibrinogen) to create fluorescence emission. These findings may provide a novel way to deliver therapeutic radionuclides for immuno-targeting purposes in the future.