The sequential development of cascade diversion-type hydropower station in the Minjiang River Basin has significantly disrupted aquatic ecosystems in downstream reduced river segments during critical fish reproductive phases. Taking Schizothorax prenanti as the research object, a generalized river channel was established based on field investigations and statistical analyses of cross-sections in its natural spawning grounds. The water depth-averaged two-dimensional hydrodynamic model was used to simulate the hydraulic habitat of spur dikes restoration section of the Schizothorax prenanti spawning ground in the generalized river channel. This article utilized the improved Vague set to evaluate the restoration effect and studied the effect of spur dikes on the microhabitat similarity of Schizothorax prenanti spawning ground. The intrinsic relationships among the suitable areas and similarity of the microhabitat of the spawning ground of Schizothorax prenanti separately and the length of spur dikes, the width of the river, the spacing of spur dikes, the flow velocity, the water depth, and the flow rate was explored by using dimensional analysis method. This analysis contributes to the construction of two response relationships between the arrangement of spur dikes and the suitable areas of microhabitat and the similarity of microhabitat in spawning ground respectively. Additionally, an empirical model for restoring the spawning ground of Schizothorax prenanti by spur dikes was constructed. The model was compared and corrected by the numerical simulation results of the downstream Moutuo town section of Jiangshe Dam in the Minjiang River Basin. The results demonstrated that after the construction of spur dikes in the generalized river channel, the water depth and flow velocity of the upstream and downstream of spur dikes rise and fall, and the action range of spur dikes was different under the conditions of different flow and the water blocking rate. When the flow is larger and the water blocking rate is smaller, the restoration effect of the spawning ground is relatively better. The comparison and verification of the numerical simulation results of the downstream Moutuo town section prove that the simulation results are relatively consistent with the empirical model. The research results provide a theoretical foundation for engineering restoration of Schizothorax prenanti spawning grounds in the Minjiang River Basin, guiding aquatic biodiversity conservation while establishing scientific references for hydraulic habitat rehabilitation in analogous fish ecosystems, thus achieving a win-win situation for river development and protection.