This invention relates to a refining method of R-(+)-alpha-phenethylammonium.IR.2S-(-)-cis-1,2-Epoxypropyl phosphonate, comprising the steps of (1) heating up distilled water or purified water to the temperature between 30 DEG C and 35 DEG C; adding crude R-(+)-alpha-phenethylammonium.IR.2S-(-)-cis-1,2-Epoxypropyl phosphonate during stirring, wherein the mass ratio of the fried crude R-(+)-alpha-phenethylammonium.IR.2S-(-)-cis-1,2-Epoxypropyl phosphonate and the distilled water or purified water is 1:4.2135 to 5.3571; (2) heating up continually to the temperature between 40 DEG C to 45 DEG C;adding active carbon; heating up continually to the temperature between 65 DEG C to 75 DEG C; preserving the temperature, wherein the mass ratio of the fried crude R-(+)-alpha-phenethylammonium.IR.2S-(-)-cis-1,2-Epoxypropyl phosphonate to the active carbon is 1:0.0169 to 0.0214; (3) filtrating to remove carbon; washing carbon cake with the distilled water or purified water to obtain filtrate; and(4) cooling the filtrate obtained in step (3) to the temperature between minus 8 DEG C to minus 2 DEG C; separating crystal; filtrating to obtain wet R-(+)-alpha-phenethylammonium.IR.2S-(-)-cis-1,2-Epoxypropyl phosphonate; drying to obtain fine R-(+)-alpha-phenethylammonium.IR.2S-(-)-cis-1,2-Epoxypropyl phosphonate; or drying the filtrate obtained in step (3) with spray drying device to get fine R-(+)-alpha-phenethylammonium.IR.2S-(-)-cis-1,2-Epoxypropyl phosphonate. The method provided by the invention has the advantages of simple technique, easy operation and good security and is beneficialfor business health, low material consumption, less pollution and low cost.