Abstract: Step-pool system is a typical bed micro-morphology in high gradient mountain rivers, which creates extremely high turbulence intensity and thus dissipates a majority the flow energy. The increase of the bed load transport intensity changed the flow field and reshaped the bedform, thus the energy dissipation effect of the step-pool system changed. A physical model of artificial step-pool system was constructed in a locally regular channel of the upper Wenxia River, a tributary of Han River in the middle Yangtze River. Experiments were conducted to study the flow field and energy dissipation in different flow discharges and bed load transport rates. Experimental results illustrated that the increase of bed load transport intensity significantly changed local flow field in the step and pool. The turbulence intensity on the step increased and the turbulence intensity in the pool decreased sharply. The increase of bed load transport intensity leaded to variation of the energy dissipation distribution. The energy dissipated by bed load transport increased, thus the energy dissipation effect of the bed structure of step-pool system decreased and the pool of the step-pool system was filled up.