Abstract: To explore the effects of different pretreatments on the extraction amount and carbon stable isotope ratio (13C) of fatty acid in Marine microalgae,the relative content and 13C values of the products of fatty acid methyl esters(FAMEs) were measured by GC/MS and GC/IRMS under the different acid catalytic condition,and then were compared and analyzed.The results show that hydrochloric acid catalysis is more suitable for fresh samples of microalgae than sulfuric acid in the process of producing polyunsaturated FAMEs; When sulfuric acid was used as catalysis,the relative contents and 13C values of FAMEs also exist certain differences in different pretreatments (A-fresh samples of microalgae,B-dry processing,C-solvent extraction) of the microalgae samples.