We report a universal chitosan-assisted method for the synthesis of Ag-included heterostructured nanocrystals in this communication. Chitosan promotes the heterostructured nucleation and growth of Ag on the intermediate nanocrystals, including single metal, alloy and heterojunction nanotubes, in which chelation probably plays a vital role. The as-prepared Ag/Pd heterostructured nanocrystals show outstanding properties when being used as bifunctional nanocomposites in label-free in situ SERS monitoring of Pd-catalytic reaction. The work not only provides a facile strategy to prepare Ag-included heterostructured nanocrystals, but also demonstrates the great potential of the bifunctional nanocomposites as a substrate for label-free in situ SERS monitoring.