Two active principles in traditional Chinese medicine Magnolia officinalis, magnolol and honokiol, were successfully separated by means of nonaqueous capillary electrophoresis. The effect of the composition of a nonaqueous buffer on column efficiency and resolution, and the effect of acid additives on peak shapes were researched. The separation was conducted with a running buffer in a mixture of methanol/acetonitrile/formamide(volume ratio: 1∶2∶2), in which the concentrations of Tris, acetic acid, and water were 60 mmol/L, 0.04 mmol/L and 5%(volume fration), respectively, and the pH(apperent pH) of the running buffer was 8.96. Magnolol and honokiol were separated on baseline within 20 min. The relative standard deviation of the analytes′ concentrations in the sample is 1.32% for magnolol and 1.60% for honokiol, and the recoveries of the spiked sample are 98.4% for magnolol and 98.0% for honokiol, respectively. Two active principles in traditional Chinese medicine Magnolia officinalis, magnolol and honokiol, were successfully separated by means of nonaqueous capillary electrophoresis. The effect of the composition of a nonaqueous buffer on column efficiency and resolution, and the effect of acid additives on peak shapes were researched The separation was conducted with a running buffer in a mixture of methanol / acetonitrile / formamide (volume ratio: 1: 2: 2), where the concentrations of Tris, acetic acid, and water were 60 mmol / L, 0.04 mmol / L and 5% (volume fration), respectively, and the pH (apperent pH) of the running buffer was 8.96. Magnolol and honokiol were separated on baseline within 20 min. The relative standard deviation of the analytes’ concentrations in the sample was 1.32 % for magnolol and 1.60% for honokiol, and the recoveries of the spiked sample are 98.4% for magnolol and 98.0% for honokiol, respectively.