Riffle‐pool constructions are common practice in river management and fish conservation, but insufficient science exists to guide objective design of riffle‐pool. Understanding the spatial design of a riffle‐pool in river systems has significant value because it can provide important information to ameliorate aquatic species decline. In this study, six types of riffle‐pool structures were designed to assess hydrodynamic and riverbed morphology effects on stream habitat status. A two‐dimensional ecohydraulic model was used to assess the roles of different riffle‐pool designs in river habitat conditions. The natural flow condition and three types of flood flow conditions were applied to the six types of riffle‐pool structures to evaluate the habitat quality and the sustainability of the riffle‐pool design in mountain rivers. The long‐term impacts of the hydrodynamic and hydromorphology conditions on river physical habitat status were also analysed. The results indicate substantial differences in habitat quality among six riffle‐pool structures. It was found that narrow riffle‐pool construction yielded the best performance for the fish habitat, which had the best habitat quality among six riffle‐pool designs with the smallest pool area. In the same riffle‐pool structure, the habitat suitability in the riffle‐pool sequence will primarily increase more rapidly and then decrease gradually along with the discharge increase. Under the flood discharge scenarios, low flood discharge could improve riffle‐pool habitat quality, while high flood discharge could fragment the riffle‐pool habitat quality further. The long‐term hydrodynamic conditions have the same effects on all six cases. Overall, low discharge and smaller pool design would be beneficial to the river system, which could help maintain habitat diversity of mountain rivers. This analysis could provide valuable information for river management and decision‐making, which could assist in designing better mountain river habitats to promote conservation and rehabilitation of endangered biota.