Coal seams in China are characterized by low permeability, high gas pressure, and soft coal, which lead to challenging gas extraction and severe gas disasters. Hydraulic flushing is widely used in the field to enhance the permeability of coal seams. Considering this fact, studying its effect on the stress and permeability variations of loaded coal is essential for upgrading the hydraulic flushing permeability enhancement technology. In the study, large-scale physical simulation experiments on hydraulic flushing were conducted to monitor stress changes in the loaded coal. On this basis, the effect of these stress changes on the permeability was investigated. The results show that the stress falls with fluctuations during hydraulic flushing, and the magnitude of decrease declines with the increase of loading stress. After hydraulic flushing, the cross-section of the hole is an ellipse, whose minor semiaxis aligns with the direction of the lower loading stress in the cross-section. Hydraulic flushing remarkably enhances the permeability, promoting it from 0.368 to 5.112 md, a rise of nearly 1,290%. During stress loading, the permeability changes over time can be divided into three stages, i.e., the compression stage, the linear elastic stage, and the transitional stage from linear elasticity to plasticity. During stress unloading, the permeability increases continuously with the passage of time, which is indicative of remarkable pressure relief and permeability enhancement effects. The permeability of the coal body does not increase linearly with the increase in perforation water pressure but instead exhibits an optimal value. The above results provide important references for optimizing the design of permeability enhancement boreholes under different stress conditions and ensuring safe production in coal mines.