<p>With increasing mining depth, the low permeability of coal seams has become a major constraint on efficient methane drainage and safe coal mining. To address this problem, this study focuses on three key issues related to hydraulic slotting/flushing in low-permeability coal seams. First, a dynamic porosity–permeability evolution equation for slotted coal is established. Second, the nonlinear relationship between permeability enhancement and coal removal volume is revealed. Third, borehole optimization criteria are proposed based on multi-physics coupling. A coupled model was developed to describe coal deformation, methane seepage, and pore structure evolution. The model links hydraulic slotting, permeability change, and the effective gas drainage radius. Field data from the Ji_15–17-13070 working face of Pingmei No. 13 Mine were used for validation. Coal removal volumes of 0.5, 0.8, and 1.2 t/m were compared. The effective drainage radius was defined by a gas pressure reduction from 0.75 to 0.6&#xa0;MPa. The results show that hydraulic slotting significantly improves coal permeability and methane drainage efficiency. At 0.8 t/m, the effective drainage radius reaches 4.02&#xa0;m after 90 days, which is 1.56 times that of a conventional borehole. The drainage radius follows a decaying power-law growth trend with time, and its growth rate decreases markedly after 90 days. Increasing coal removal volume further enhances permeability, but the gain is nonlinear and gradually weakens. Based on the calibrated model, borehole spacing schemes were optimized for three-pattern and four-pattern layouts. Industrial tests show that the prediction error is less than 0.2&#xa0;m. The model therefore provides a reliable tool for slotting parameter selection and borehole layout design. These findings support efficient methane drainage and borehole layout optimization in low-permeability coal seams.</p>