Abstract: Concrete lining is a widely adopted engineering measure to improve water conveyance efficiency of irrigation canals, while cracking of concrete lining will induce severe seepage loss during water delivery, which drastically reduces irrigation water use efficiency and triggers a vicious cycle of canal seepage, frost heave of foundation soil, and further lining cracking in seasonally frozen regions. Previous studies mainly focused on the influence of cracks on the durability and safety of concrete structural members, with limited attention to the seepage hydraulic characteristics and leakage mechanism of cracked lining under actual canal operation conditions. To address this gap, this study investigated the permeability evolution law of cracked concrete lining and the hydraulic features of canal leakage, based on the fundamental theory of water flow in single cracks and the Poiseuille seepage model. A series of constant-head permeability tests were conducted on prefabricated cracked concrete specimens, to quantify the effects of crack width, lining thickness and water head on lining permeability, with 63 working conditions covering crack widths of 0.1～3 mm, lining thicknesses of 60,70,80 mm, and water heads of 200,400,600 mm. Grey correlation analysis was applied to rank the significance of influencing factors, and a multivariate nonlinear regression model for permeability prediction was established. Furthermore, a three-dimensional fluid-solid coupling numerical model for U-shaped irrigation canals was developed, with cracks equivalent to ideal porous media, and the model reliability was verified through physical tests. The experimental results show that crack width is the dominant factor affecting permeability, which increases with crack width in a trend of rapid first and then slow. When the crack width is less than 0.5 mm, the permeability evolution conforms well to the Poiseuille seepage model, with minimal sensitivity to water head and lining thickness. For crack widths exceeding 0.5 mm, permeability decreases with the increase of water head and lining thickness, due to the prominent nonlinear flow effect and increased flow path resistance. Grey correlation analysis confirms that the correlation with permeability ranks as crack width > water head > lining thickness, and the established regression model achieves a high correlation coefficient R² of 0.998. Numerical simulation results indicate that the seepage velocity at cracked areas is far higher than that of intact lining. When the crack area accounts for only 1% of the total lining area, the maximum contribution rate of cracks to total seepage reaches 65.1%. The water flux inside the crack presents a parabolic distribution (maximum at the center and minimum at the edges), and a negative pore pressure growth zone is formed at the crack, which acts as the core seepage channel. Cracks closer to the canal bottom show faster and more stable seepage development.