The invention discloses a heparanase III fusion protein and a coding gene and an expression method thereof. The fusion protein of the invention (named as MBP-HepC) is a protein in a) or b): a) a protein consisting of amino acid sequences shown by the 1-1028th site of a sequence 2 in a sequence table; and b) a protein derived from a), provided with heparanase III activity and obtained by substituting and / or deleting and / or adding one or more amino acids in an amino acid sequence of the sequence 2 in the sequence table. The coding gene of the protein is also within the protection range of the invention. By introducing the gene into protein heparanase expressed in recombinant escherichia coli, the enzymatic activity can reach 1,776.3 IU per liter of fermentation liquid, the expression amount can reach 240 mg per liter of fermentation liquid, and the specific enzymatic activity can reach 7.39 IU / mg. The invention also can realize further purification of the fusion protein through affinity separation.