The estimation of boundary shear stress distribution in a channel is a challenge in some hydraulic or environment investigations. A new partition model of a trapezoidal cross-section in a prismatic channel with composite roughness has been introduced based on a concept of a standardized cross-section using the “zero-shear stress” division lines. Based on this new model, an “equal local-region velocity” assumption, which can be regarded as an improvement of Einstein’s (1942) “equal velocity” assumption, has been proposed that is based on a discussion on the mechanism of energy transfer and velocity distribution at two sides of a dividing line. This assumption along with some empirical treatments have been employed to establish a new method to estimate the boundary shear stress of a side-wall or bed. Comparisons show that the proposed method can be applied to composite roughness cases and provides better prediction performance compared to other methods.