Abstract: The configuration of stepped channels in mountainous streams is influenced by the complex hydraulic characteristics,like the inflow,sediments and the larger slope river-bed. To further study its resistance mechanism,a new roughness height formula is derived and applied for the stepped channels by expanding the theory of roughness height of stepped channels configuration from the dimension of the hydraulic radius. The expression of Darcy-Weisbach form factor for the napping flow of the stepped channels is deduced. Thus the formula of total resistance factor is obtained from sources of resistance components. The results of the new formula shows that the error between the total flow resistance factor calculated from the three components and the actual field measured data is small based on the field data of different river sections. With the increase of Reynolds number and the size of step element,the resistance factor of sediment particles on the riverbed surface basically-stabilize at a certain. With the spill flow formed by the stepped riverbed configuration changing into the skimming flow,the resistance coefficient of the body gradually decreases,and the resistance factor of the flow generated by the larger loose boulder descends with the increase of Reynolds number.