Abstract: The milk of Saanen Goat and Holstein Cattle were used as the material to investigate the fat content and fat globule size by Rose Gottileb method and laser light scattering respectively.The Lipoprotein lipase activity and the free fatty acids which were separated from the milk fat were researched using the chromatographic column containing alumina and silica gel as measured by lipase activity analysis in clinica and the gas chromatograph mass spectrometer respectively.The results showed that the fat content of Saanen Goat milk and Holstein milk were4.04,3.55 g /100 m L respectively,the mean fat globule size were 3.46,3.16 μm respectively,the linear and positive relationship was found in the milks between fat globule size and fat content. The Lipoprotein Lipase activity in Saanen milk and Holstein milk were 229.62 ± 9.31,( 366.81 ± 24.33) U / L,the distribution of Lipoprotein Lipase of Saanen milk and Holstein milk in the cream phase was 51.35% and 27.09%,in skim milk were 48.65% and 72.91%.The total free fat acids from Saanen Goat and Holstein Cattle were 211.38 and 717.02 mg / kg,the short chain free fat acids were 22.05 and 205.51 mg / kg. The caproic acids and caprylic acid were the main effect flavour components in Saanen goat milk.