Epothilones are a kind of poliketide macrolide with antifungal and anticancer bioactivity which are attracting more and more attention. In this paper we compared the extraction effects of epothilones with several organic solvents by comparing the recovery rates and purities. Result shows that chloroform and dichloromethane are more suitable for the extraction of epothilones than methanol which is universally used. Then we analyzed the HPLC and TLC results of the different solvents extract, and optimized the extraction method by using chloroform and ether. The final recovery rate and purity increase 114.2% and 21.53 times than methanol.