Abstract: Influenced by traditional vertical-slot fishways, previous studies on nature-like fishways generally adopted a relatively uniform energy dissipation cross-section, and the analysis of hydraulic characteristics often relied on the cross-sectional average velocity. This paper focused on the nature-like fishway with staggered permeable stone walls. To systematically understand the advantages of its hydrodynamic characteristics and the influence of design parameters on the energy dissipation rate, a physical model experimental research was carried out considering the vertical stratification of the flow field along the water depth. The results show that through coordinated optimization of hydraulic conditions, this type of fishway forms a smooth and straight upstream passage on the surface layer that supports fish passage across the entire cross-section; in the middle and bottom layers, under the combined effects of flow around the walls and flow through the pores, an "S"-shaped passage with low energy consumption and low curvature is formed, providing a clear upstream direction. The interaction between the pore flow and the flow around the wall not only eliminates the recirculation zone behind the wall but also creates a low-velocity resting area, thereby effectively avoiding the risk of disorientation for upstream migrating fish caused by the fixed path and recirculation phenomena in traditional vertical slot fishways. The energy dissipation rate (η) is regulated by three factors: the flow rate (Q), the bottom width of the cross-section (B), and the relative relationship between the stone wall height (H) and the water depth (h). The energy dissipation rate shows a significant negative correlation with the flow rate. At low flow rates, increasing the bottom width enhances frictional energy dissipation efficiency; however, as the flow rate increases, the advantage of increasing the bottom width in improving energy dissipation efficiency diminishes rapidly. The influence of the wall height-water depth relationship on the energy dissipation mechanism can be divided into three stages: in the non-submerged stage, the difference in energy dissipation rate is not significant; in the critically submerged stage, the energy dissipation rate is positively correlated with water depth; in the over-submerged stage, weir flow dominates, leading to an accelerated decline in energy dissipation efficiency. Overall, the nature-like fishway with staggered permeable stone walls features layered synergistic hydrodynamic characteristics and diverse energy dissipation mechanisms, thereby overcoming the inherent shortcomings of traditional fishways. The results can provide a reference for the engineering practice of nature-like fishways.