The invention discloses a recombinant protein of a human fibroblast growth factor 21 as well as a preparation method and application thereof. The preparation method comprises the following steps: linking a nucleotide sequence of a coding gene of the human fibroblast growth factor 21 recombinant protein with an expression vector to obtain a recombinant expression vector; transforming the recombinant expression vector into host cells, screening high-expression positive host cells, culturing the cells, inducing the cells to express the human fibroblast growth factor 21 recombinant protein, collecting thalli, breaking, and carrying out centrifuging, clarification and purification, so as to obtain the target product, namely the human fibroblast growth factor 21 recombinant protein. The invention further discloses application of the human fibroblast growth factor 21 recombinant protein in the preparation of drugs for treating metabolic diseases. Compared with a wild hFGF21 protein, the human fibroblast growth factor 21 recombinant protein (mFGF21) has the advantages that the activity is remarkably improved, and the blood glucose level in a diabetic mouse can be relatively effectively reduced.