The performance of the seepage control structure directly affects the safe operation of the dike when it is constructed on a permeable foundation with long stretch. According to the engineering geological conditions of the long dike in the Huduxi Project reservoir area on the Minjiang River, the layout of the high-pressure jet grouted cut-off wall at the dike foundation is optimized and analyzed using the three-dimensional seepage analysis method. Calculation results show that the high-pressure jet grouted cut-off wall can effectively reduce the groundwater level and the leakage of reservoir water to the protected low-lying area behind the dike, but its seepage control effect is affected by the spatial distribution length, depth and permeability of the seepage control structure and the permeability anisotropy of the stratum materials. The minimum spatial length of the cut-off wall that meets the requirement of no overflow in the protected low-lying area decreases with the increase of its layout depth and the improvement of construction quality. The seepage control effect is obvious when the hydraulic conductivity of the cut-off wall is lower than 1×10-5 cm/s and the strong permeable stratum is cut off; however, further enhancement of the construction quality and layout depth does not significantly improve the seepage control effect. The permeability anisotropy has little influence on the improvement of the seepage control effect caused by the enhanced construction quality of the cut-off wall, whereas increasing the layout depth has a great influence on the seepage control effect and the optimization design of seepage control structure when the permeability anisotropy is relatively large. With the increase of the material permeability anisotropy ratio, the required minimum spatial length of the cut-off wall increases gradually from 180 m under the isotropic case to 220 m. Moreover, when the permeability anisotropy ratio is relatively large, it may be necessary to increase the depth of the cut-off wall.