In order to analyze the content of fatty acid methyl esters, biodiesel was analyzed by gas chromatography method. Biodiesel was produced from the raw materials soybean oil and mussel shell catalysts. GC analysis was developed by using HP-innowax chromatographic column and FID detector. Undecanoic acid methyl ester was chosen as internal standard solution. The results show that five kinds of fatty acid methyl esters were linear at range 4 g•L-1～31 g•L-1 (γ≥0.9928). The average recovery rate was 98.28%～101.85%, and relative standard deviation was less than 0.31%. The coefficient of variance of precision was less than 1.59%. This GC method is simple, rapid and accurate and it will be the base for further research.