Flow resistance in a natural stream is caused by complex factors, such as the grains on the bed, vegetation, and bed-form, reach profile. Flow resistance in a generally stable gravel bed stream is due to protrudent grains from bed. Therefore, the flow resistance can be calculated by equivalent roughness in gravel bed stream, but estimation of equivalent roughness is difficult because nonuniform size and irregular arrangement of distributed grain on natural stream bed. In previous study, equivalent roughness is empirically estimated using characteristic grain size. However, application of empirical equation have uncertainty in stream that stream bed characteristic differs. In this study, we developed a model using an analytical method considering grain diameter distribution characteristics of grains on the bed and also taking into account flow resistance acting on each grain. Also, the model consider the protrusion height of grain.