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The crude milk thistle oil was refined and degummed using membrane separation technology and the process was optimized. Taking flux and degumming as the main indicators, and referring to indicators such as iodine value, peroxide value, acid value, etc., inorganic alumina ceramic membranes with pore sizes of 300, 800 nm and 1 μm and organic membranes with a molecular weight cut-off of 10 kDa were screened. Three organic membranes including polyamide (PAN) membrane, cellulose acetate (CA) membrane and polyethersulfone (PES) membrane were screened, and membrane materials with low membrane pollution, high degumming rate and moderate flux were screened out. The selected PES membrane was optimized by orthogonal process in terms of membrane molecular weight cut-off, pressure and oil-soluble ratio. The composition of fatty acids before and after refining was compared with a gas-mass spectrometer, and the morphology of the membrane before and after the experiment was observed by scanning electron microscope (SEM). The results showed that the degumming rate of PES membrane was 73.33%, the flux was 14.69 L·m−2·h−1, the iodine value was 111.1 g/100 g, the peroxide value was 0.115 g/100 g, and the acid value was 5.7 g/mg. The overall effect was the best. The conditions of the membrane after orthogonal optimization were the membrane molecular weight cut-off of 8 kDa, the oil-soluble ratio of 1:3, and the pressure of 0.3 MPa. RSD was 1.93%