In order to study the flow characteristics in wide and narrow alternated channels under different discharges, we chose upstream reach of Baoxing river as research object and established a three-dimensional flow numerical model through simplifying the actual river. Results show that 1) under low discharge, backwater at upstream reach of narrow section was not obvious, and wide and narrow alternated channel showed characteristics similar to straight channel; 2) with the increase of discharge, backwater in the upstream reach of narrow section was intensive, and the distribution of cross-section average velocity showed a multi-stage regularity (stages of increasing, relatively stable, rapidly decreasing, relatively stable and finally increasing);3) affected by river width, backwater and reflux, cross-section flow characteristics in wide section was more complex than that in narrow section, and the velocity distribution at backwater area was obviously different from that at non-backwater area;4)under different discharges, dramatic changes of bed shear stress in wide section will lead to discontinuous movement of pebbles, and deformation of riverbed in wide section showed cyclical tendency, which is in favor of stability of the wide river bed structure; 5) while in the narrow section, riverbed structure was compatible with surrounding environment under long-term larger bed shear stress, then larger flow energy in narrow section can be expended and riverbed stability can be guaranteed.