The present invention provides an optimized recombinant flagellin protein and preparation and use thereof. The protein is with a deletion in the hypervariable region, said hypervariable region is the region from 180 to 400 amino acid of the flagellin protein, and the proteins include FliCΔ190-278, FliCΔ220-320 or FliCΔ180-400. The method of preparing said protein, comprising introducing a deletion into the hypervariable region of the flagellin protein. First constructed the flagellin protein recombinant plasmid, and then used it as template to construct the flagellin deletion cloning, and expressed and purified. The present invention also provides the use of the recombinant flagellin protein as adjuvant. The recombinant flagellin protein in present invention decreases the potential risks it may have, and decreases its antigenicity and immunogenicity and the inflammatory response induced by it, through deleting its main areas of immunogenicity and antigen activity.
