Abstract: Small hydropower projects and other anthropogenic activities have altered the natural hydrological regimes of mountain river systems, thereby degrading native fish habitats. To explore feasible and effective habitat restoration strategies for mountain river fish, this study selected the Xingfu River, a first-order tributary of the Heishui River, as the study area. Targeting Schizothorax prenanti, a representative endemic fish species, we identified and designed a suite of habitat restoration measures with specific dimensions, and proposed a multi-measure synergistic restoration scheme for creating suitable habitats for this species. An in-situ field experiment was implemented to validate the scheme. We constructed a two-dimensional hydrodynamic model coupled with a fish habitat suitability model to quantitatively evaluate restoration effectiveness in terms of physical habitat conditions. The habitat suitability index (HSI) and weighted usable area (WUA) were computed as primary metrics. Additionally, passive integrated transponder (PIT) telemetry was employed to track individual fish movements and behavior before and after restoration. Our results demonstrate that the multi-measure synergistic scheme, integrating boulder placement, pool-riffle sequences, ecological groynes, ecological mid-channel bars, and large woody debris with rootwads, significantly improved habitat quality for S. prenanti. Under a discharge of 0.5 m³/s, the scheme elevated the average HSI from 0.60 to 0.69, and increased the WUA from 282 m² to 324 m², representing a 15% enhancement, while the area of highly suitable habitat doubled. At a discharge of 1.0 m³/s, the average HSI improved from 0.73 to 0.81, and the WUA rose from 341 m² to 378 m², an 11% increase, with the highly suitable habitat area expanding by 0.5 times. As discharge in the experimental reach increased, both the average HSI and WUA of the restored reach initially rose and then declined, reaching maximum values of 0.83 and 390 m², respectively, at a flow rate of 1.5 m³/s. At this discharge, the highly suitable habitat area amounted to 318 m², which represented a threefold increase relative to the pre-restoration condition at 0.5 m³/s. Among all implemented measures, ecological gravel bars/shoals were identified as the most preferred restoration structure for S. prenanti, based on both habitat suitability indices and fish tracking data. The PIT tracking results corroborated the model predictions, showing higher fish residency and activity within the restored zones, particularly around the ecological shoals and pool-riffle complexes, indicating behavioral selection for the newly created habitat features. The integrated approach not only enhanced habitat heterogeneity by diversifying flow velocity and water depth gradients but also improved shelter availability and foraging opportunities, which are critical for the life cycle of S. prenanti. Furthermore, the study revealed that the effectiveness of individual restoration measures varied with flow conditions; while boulders and woody debris provided stable cover during low flows, ecological groynes and shoals played a more significant role in creating velocity shelters and feeding grounds during moderate to high flows, highlighting the importance of combining multiple structures to ensure functional resilience across a range of hydrological scenarios. The synergistic effects among different measures were evident: the pool-riffle sequence facilitated aeration and nutrient cycling, boulders generated localized turbulence that attracted benthic prey, ecological groynes deflected flow to maintain pool depth, and woody debris offered both structural complexity and organic matter retention. This complementarity underscores the necessity of a holistic restoration design rather than the isolated application of single measures. Our findings also suggest that the optimal discharge range for the restored habitat lies between 1.0 and 1.5 m³/s, which corresponds to the typical baseflow conditions during the spawning and rearing seasons of S. prenanti in the Heishui River basin. Therefore, the proposed restoration scheme is hydrologically and ecologically aligned with the natural flow regime of the regional context. This study provides a scientific reference and a typical demonstration for the restoration of suitable habitats for S. prenanti in the Heishui River basin, and offers valuable insights into the design, modeling, and field evaluation of integrated physical habitat restoration in mountain streams affected by small hydropower operations.