The citrinin binding capacity of muscle protein from bullfrog (Rana catesbeiana) immunized with citrinin-bovine serum albumin (BAS) conjugate emulsified with Freund’s complete adjuvant was investigated. The protein with high citrinin binding capacity was embedded into sodium alginate microspheres. The optimum conditions were determined as follows: immunogen dosage 6.4 mg, sodium alginate concentration 4 g/100 mL, CaCl2 concentration 5 g/100 mL, glutaraldehyde concentration 0.2%, and crosslinking time 2 h. Two milliliter of the crude citrinin extract from red rice was passed through a column packed with 2 g of sodium alginate microspheres followed by washing with 20 mL of ultra-pure water to remove the impurities, and good chromatogram was obtained without interfering peaks compared with commercial immunoaffinity column. The recovery of citrinin standard solution eluted with 5 mL of 70% acetonitrile and trifluoroacetic acid mixture was 86.7%. The column capacity was 0.101 μg/g. The content of citrinin in red rice was determined to be 0.037 and 0.043 μg/g using the column developed in this study and commercial immunoaffinity column, respectively. However, further study should be done to improve the preparation process for better product performance.