Citrus is an important horticulture. However consumption of citrus fruits could cause allergen for some people. With the method of Jameson-Wolf, Kyte-Doolittle, Emini and Karplus-Schulz, the antigenicity, hydrophilicity, protein surface accessibility and flexibility of citrus allergen protein PGIP (polygalacturonase inhibitor protein) were predicted. Meanwhile PET-28 a-PGIP vector was constructed, and then transfer to Escherichia coli. The target gene was induced and expressed. The results showed: When the secondary structure of amino acid was β-angle and irregular curl, the antigen index>0, the flexibility>0, the hydrophilicity>0, the protein surface accessibility>1 amino acid region, the sequences of the B cell epitope binding amino acid were 19~22, 37~41, 49~52, 68~69, 117~120, 163~164, 173~177, 221~226, 236~240. By estimating the amino acid region, it provides support for finding the best possible region of the B cell epitope of citrus allergen protein PGIP, and also provides a theoretical basis for the further study of citrus allergen protein PGIP.