The isomerization of methyl ester of cottonseed oil under the catalyst iodine was investigated. By the methods of GC-MS and UV, the constituents of isomerized products were analyzed. Under the optimum isomerization conditions, mass fraction of conjugated linoleic acid in isomerized cottonseed oil methyl esters was 31.2%, and conversion of conjugation was 56%. UV absorbancy curve of measured samples at different concentration was plotted, and lineal' relationship of absorbancy and samples' concentration was determined. Combined the accurate concentration of conjugated linoleic acid by GC-MS, the empirical formula for the quantilation of conjugated linoleic acid in isomerized products was obtained, omega_(conjugated linoleic acid)=0.0080l'A/C. The absorbance constant was 0.00801, optimum mass concentration was 0.02～0.04g/L, and error was less than 5%. The results show that UV is a simple and quick metliod for determination of conjugated linolleic acid in isomerized cottonseed oil methyl esters.