Abstract: Used by strong polarity column Wondacap-wax, Rt -2560 and medium polarity column Rt -1701, for 37 fatty acid methyl esters ( FAMEs) was compared by gas chromatography-flame ionization detector ( GC-FID) .A better detection was established and camellia seed oil of laboratory were detected. The results showed that changing the temperature, the heating process and the rate of temperature speed could improve the separation degree of mixed standard. The high polarity chromatographic column was more suitable for the separation and detection of fatty acids in oil and fat than the medium polarity chromatographic column.Rt -2560 column separation effect was slightly better than Wondacap-wax column, the medium polarity part Rt -1701 might be more suitable for some functional fatty acids composition, should not be used for the separation of fatty acid 37 kinds of standard.