Many rivers are subject to ice-covered flow conditions in cold climate regions or during the winter months. The presence of ice cover can change stream flow hydrodynamics and thus affect the hyporheic exchange involved in many biogeochemical processes in aquatic environments. Among the various features of ice cover, its underside roughness is a main factor modifying the surface–subsurface flow hydrodynamics. To date, there has been little research on how ice cover affects the hyporheic exchange, even less on the effect of the ice cover roughness. This leaves open questions on the mechanical changes initiated at the ice-water interface and transferred to the water–sediment interface. In this study, a coupled surface–subsurface computational approach was used to model conjunctively the channel flow over dune bed and the underlying porous flow under different ice cover conditions. The results show that ice cover can enhance the hyporheic flux and reduce the hyporheic zone depth when compared to open channel flow at equivalent discharge. As the river flow depth increases to 4 times the height of the dune, the effect of the ice cover on the hyporheic flow becomes negligible. Within this effective range, the hyporheic flux via the channel water depth follows a power-law function. Ice cover roughness greatly augments the exchange rate while compresses the exchange space, therefore reduces flow residence time in the hyporheic zone. Based on the modeling results, prediction models were proposed for evaluating the impacts of ice cover roughness on the hyporheic exchange flux and depth. Our study indicates that hyporheic flow exchange is significantly impacted by the roughness of the ice cover which in turn the hyporheic exchange is likely to affect the river ice processes as well as the water quality and ecological functions throughout the river corridors.