Abstract: As a raw material, 2 oxocyclohexaneacetate was hydrolyzed into 2 cyclohexaneacetate. Then its carboxyl groups were protected by substituted benzyls with substituent groups including electron withdrawing group nitro, electron donating group methyl and comparative group hydrogen on the para side of benzyl. By Baeyer Villiger oxidation, 2 or 6 carboxyl functionalized polycaprolactones were generated at the same time. Afterwards, the isomers were isolated and purified using flash chromatography to obtain 6 carboxyl functionalized polycaprolactone with high purity. The electronic effect of substituent groups on the protecting groups led to the formation of isomers in different rations. A maximum rate of 6 substituted compound was obtained with the existence of electron donating group. Moreover, the difference in polarity of substituent groups affected the separation of isomers. Larger difference in polarity resulted in an easier separation.