Abstract: Saturated fatty acids and their isotopic composition are important proxies to reconstruct paleoenvironment and paleoclimate. There are several extraction and purification procedures of n-fatty acids based on different principles. However, a comparison test between different processes has not been reported. In this article, the agreement of fatty acid and its isotope compositions purified by different processes directly impacted on the proxies′ application, especially on the comparison of reconstruction results from different regions in global change research. Two common fatty acid purification procedures were used to purify lipids of fatty acid standards, plant and peat samples. For the standards, the recovery rates of these two procedures were all greater than 85%, which indicates that these two methods are reliable to process the n-fatty acids. However, for the plants and peats samples, Procedure 1 obtained a relatively large amount of shorter chain length n-fatty acids. According to our results, Procedure 2 obtained almost all of the free fatty acids, while Procedure 1 can obtain both the free and ester state n-fatty acids in the samples. Since the free state fatty acids and esters state fatty acids in the sediment can be transformed into each other, using Procedure 1 to analyze the total fatty acids in the sediment sample was more appropriate. Alternatively, we can also use the Procedure 2 after the ester-state fatty acids in the lipids were released as free state acids by saponification.