Reservoir construction changes a river's natural flows and temperature, thereby threatening fish migration. Researchers have tried to restore fish migration passages by ensuring environmental flows in downstream river channels. However, reservoir impoundment changes upstream environments from lotic to lentic and thereby hinders fish migration by eliminating migration cues, which has been rarely considered. This study characterized the invisible barriers that large reservoirs create for migratory fish. Water currents are the primary orientation cues for migration due to fish's natural rheotactic tendency. Fish also require suitable temperatures during migration. We built a quasi‐3‐D model to simulate hydrodynamic and temperature conditions in large reservoirs and tested whether these conditions met the velocity and temperature requirements of fish. Due to the strong effects of operation on reservoir conditions, we proposed an eco‐friendly technical operating solution to restore migration passages. We added an ecological constraint (i.e., creating a suitable velocity field for fish migration) to reservoir operation model and applied multiobjective optimization to simultaneously protect reservoir benefits. As a case, we applied our approach to China's Danjiangkou Reservoir. We found that velocities in more than half of the zones along the potential fish migration route through the reservoir were lower than the fish requirement and could not offer orientation cues for migration. The eco‐friendly operating scheme effectively restored a fish migration passage by managing reservoir releases during key migration periods, slightly reducing the reservoir's socioeconomic benefits by 1.67–5.03%. This study provides a new perspective on biodiversity and fisheries protection in global regulated rivers.