The invention discloses a method for separating purified cytidine diphosphate choline by hydrophobic chromatography. The method comprises the following steps of: (1), performing enzyme inactivation, centrifugation and ultra-filtration of a cytidine diphosphate choline conversion liquid; (2), after adjusting the pH of the pre-processed cytidine diphosphate choline conversion liquid to between 2.0 and 14.0, adding an inorganic salt to prepare column-loading liquid which contains 0.01 to 5mol/L of inorganic salt and 0.1 to 40g/L of cytidine diphosphate choline with the cytidine diphosphate choline conversion liquid, absorbing the column-loading liquid with a hydrophobic chromatography resin and eluting with pure water of which the pH value is 2.0 to 14.0; and (3), nano-filtering, desalinating and concentrating the eluate, and obtaining the cytidine diphosphate choline through crystallization. In the method, the separation process is simple; through regeneration, the resin after elution can be repeatedly used; the separation cost is low; the product is easily crystallized; and the CDP-choline product with high purity and high yield can be obtained.