Understanding the adaptive relationships between fish morphology and water flow and leveraging this knowledge to shape water flow conditions beneficial for the conservation of rare fish are critical for their protection. This study integrates a high-precision fish model with a wave equation motion framework to accurately analyze and visualize the forces acting on various parts of fish bodies during swimming. The results quantitatively reveal the trade-offs in resistance and propulsion between two fish morphologies. For Carassius auratus, a propulsive force advantage is observed within a velocity range of 0-0.6 m/s, while Schizothorax prenanti demonstrates a staged propulsive advantage as velocity increases. Specifically, S. prenanti achieves maximum propulsion more rapidly at 0.4 m/s, maintains higher propulsion values at 0.6 m/s, and demonstrates adaptability to water velocities of 1 m/s, which prove insurmountable for C. auratus. Furthermore, a detailed analysis uncovers a strong correlation between fish morphology and biomechanical performance. The long-term adaptation of S. prenanti to flowing water environments is driven by its low-resistance morphology, enabling it to dominate despite generating less propulsion than C. auratus. Conversely, C. auratus, adapted to low-flow environments, prioritizes strong propulsion at the cost of heightened resistance in high-flow conditions. This study establishes a morphology-biomechanics-flow environment framework, enabling researchers to design flow conditions that align with the mechanical advantages of target fish species. Such an approach offers a novel perspective for fish habitat management and conservation.