Abstract: To improve the quality of microalgae DHA oil, these methods of β-cyclodextrin, Silica gel and molecular distillation were respectively adopt to remove the cholesterol in the oil. Effects of the three methods on the acid value, peroxide value, oxidative stability and fatty acid composition were measured. The result indicated that cholesterol reduction reached 50%, higher than the 33% of silica gel method and 22% of molecular distillation method. Moreover, compared with the other two methods, method of β-cyclodextrin decreased oil acid value and improved the oxidative stability apparently, and had little effect on the fatty acid composition. The comparison showed that β-cyclodextrin met the requirements for the future removal of cholesterol in microalgae DHA oil refining process.