The separation mechanism for neutral solutes on a cyano column in capillary electrochromatography (CEC) was investigated and the effects of components of mobile phases and the kinds of buffers on retention of samples were studied. In comparing the separation behavior of samples on CN column with reversed-phase ODS column and normal phase SI column, the peak order was different on CN column under different experimental conditions, and the characteristics of CN column having both reversed and normal phase mechanisms were obvious. The migration velocities for neutral solutes of different polarity on CN column were very different by the effects of two mechanisms under different operating conditions. It is easy to change peak order and to adjust selectivity.