A heparin-binding protein having covalently bonded heparan sulfate sugar chains within its molecule is produced by ligating a cDNA encoding a peptide which can be modified with heparan sulfate sugar chains selectively to a cDNA encoding a heparin-binding protein and producing in an animal cell the gene product of the resultant ligated cDNA. This heparan sulfate sugar chain-modified heparin-binding protein is functionalized by covalently bonding thereto glycosaminoglycan sugar chains containing little chondroitin sulfate. For example, this heparin-binding protein is excellent in stabilities, such as thermostability, acid resistance, alkali resistance and in vivo stability. Further, the heparan sulfate sugar chain-modified heparin-binding protein is effective in cell proliferation and tissue regeneration, and has effect of regulating the physiological functions of FGFs. Thus, this heparin-binding protein is extremely useful as a medicine for preventing or treating various FGF-related diseases.