This paper presents a new method for the system identification of channel roughness for the water diversion projects. According to the principle of hydraulics, established the relationship among channel roughness, rough height ks and hydraulic radius R, and deduce the linear model by means of the mathematical transformation to make use of the least square method for the identification. Finally, based on the prototype observation data from the south to north water diversion project and considering the influence of channel section shapes, bottom slopes and lengths etc, a universal formula is obtained for calculation of channel roughness by the system identification.