Achieving a harmonious alignment between the biological characteristics of fish and hydrodynamics patterns is crucial for ensuring the efficacy of fish passage facilities. In this study, based on the hydrodynamic characteristics of the river and the biological characteristics of fish, we evaluated the internal flow field in the nature-like fishway of Congen II hydropower station located along the Chabao river and explored methods to improve the operation efficiency. Based on comprehensive considerations of the flow field, turbulent kinetic energy, and the migration pathways of fish, it is found that the implementation of a continuous oblique bottom slope represents a more cost-effective and operationally convenient solution. The influence of different permutation of bulkheads in the nature-like fishway on operational efficiency was further examined. Our investigation revealed that the nature-like fishway with the continuous slope of 2% and the arrangement of three bulkheads in each row (model 3) exhibited a relatively simple velocity distribution and linear flow line, which poses challenges for fish in locating resting areas. In addition, the distribution of low turbulence kinetic energy area in the mainstream made it less favorable for fish to transition from the mainstream to the rest area within the fishway. The nature-like fishway with the continuous slope of 2% and the arrangement of two or three bulkheads in staggered rows (model 4) demonstrated better performance. Several potential fish migration routes for both model 3 and model 4 were proposed based on the numerical simulation results. In model 3, fish exhibited a continuous sprint through the concentrated high-speed area, which was less favorable for fish to rest and forage. In contrast, model 4 exhibited a diversified flow velocity distribution, enabling fish to make timely changes in their direction during migration. This feather proved to be advantageous in enhancing fish migration within the passage. The design of nature-like fishway in this study provides an important reference and technical support for the construction and optimization of the nature-like fishway for low dams, and is of great significance for restoring river connectivity destroyed by small hydropower construction and improving fish migration.