The invention discloses a method for separating swainsonine by using counter-current chromatography. According to the invention, methyl tert-butyl ether, n-butanol and water are mixed and then stood for layering so as to form a solvent system for a counter-current chromatographic stationary phase and a counter-current chromatographic mobile phase; the stationary phase is pumped into a separation column of a counter-current chromatographic instrument at a great flow velocity; after the separation column is full of the stationary phase, the instrument is started, the main engine of the counter-current chromatographic instrument is allowed to rotate at a set rotating speed, and then the mobile phase is pumped into the separation column at a certain flow velocity; after the two phases reach dynamic balance in the separation column, sample introduction is carried out through a sample introduction valve; fractions are collected by an automatic fraction collector; and thin layer chromatography and high performance liquid chromatography are used for detection, fractions containing a swainsonine component are combined together, then a solvent is recovered, and recrystallization is carried out so as to obtain swainsonine with a purity greater than 90%. The method provided by the invention has the advantages of easiness, convenience, fastness, a good separation effect, a great preparation quantity, small loss of a sample, low separation cost, high product purity and suitability for industrial production.