Many uncertainties such as variable irregular structure and complex flow conditions bring difficulties to the design of a nature-like fishway. This study defines the main factors and parameters affecting flow conditions such as permeability ratio, offset ratio, bottom slope and pool length to simplify and generalize the irregular geometry of the nature-like fishway. According to the engineering requirements of the Mopiling nature-like fishway, the effect of the above parameters of pool geometry on the flow structure is investigated through a 3D turbulent numerical simulation, and the parameter thresholds are summarized according to the optimization of the flow conditions. The results show that under the same conditions, the maximum velocity of the control section increases with the increase in permeability ratio, bottom slope and pool length, and the offset ratio has limited effect on the maximum velocity of the control section. It is recommended that when the bottom slope is 1/250 and the pool length is 10 m, the permeability ratio should not be greater than 0.30 and the offset ratio should be located between 0.15 and 0.60. When the bottom slope is adjusted to 1/200, it is recommended to control the permeability ratio below 0.20, the offset ratio between 0.30 and 0.60, and the pool length can be adjusted to 8 m. Within the above threshold range of the design parameters, the maximum velocity in the fishway can be basically controlled at about 1.0 m/s. The mainstream in the pool is clear and the flow pattern is good, which can basically satisfy the requirements of fish passing. The relevant design parameters and optimization strategies can provide reference for similar projects.