The invention provides a preparation method of a morpholine derivative represented as the formula (I), wherein the preparation method includes the steps of: (1) dissolving trialkyl (aryl) phosphine, azodicarboxylic acid diester, (R)-1-(3,5-bis(trifluoromethyl)phenyl)ethyl-1-ol, and (R)-4-benzyl-2-hydroxyl-morpholine-3-one in a reaction solvent; (2) adding the azodicarboxylic acid diester so that the trialkyl (aryl) phosphine and the azodicarboxylic acid diester are subjected to an addition reaction quickly in the reaction solvent to generate zwitter-ions, which are then converted into quaternary phosphonium salt by means of a hydrogen proton supplied by the hydroxyl group in the (R)-1-(3,5-bis(trifluoromethyl)phenyl)ethyl-1-ol; (3) enabling the hydroxyl group on the 2-position of the (R)-4-benzyl-2-hydroxyl-morpholine-3-one to be reacted with the quaternary phosphonium salt to generate morpholine oxy-phosphonium salt; and (4) with the (R)-1-(3,5-bis(trifluoromethyl)phenyl)ethyl-1-ol, which loses the hydrogen proton, as a nucleophilic reagent, performing an SN2 reaction with the morpholine oxy-phosphonium salt to obtain a product which has turned configuration. The method has high stereo-selectivity, avoids generation of an isomer byproduct during the reaction process, and reduces the load of separation and purification of the product in the later period.