Abstract: Water-locking flocs formed by ultrafine tailings particles will damage the thickener underflow concentration in the thickening process during paste preparation. The relationship between the mesostructure and seepage characteristics of tail mortar is typically ignored when investigating the deep dehydration stage. A shearing seepage test of an unclassified tailing–sedimentation bed was performed with copper tailings, and the morphology and geometric distribution of micropores were analyzed via X-ray computed tomography. Moreover, the shearing evolution of the micropore structure and seepage channel was investigated to evaluate the dewatering performance of underflow slurry using a three-dimensional reconstruction approach. The results show that porosity decreases considerably under shearing. The connected-pore ratio and the average radius of the throat channel reach peak values of 0.79 and 31.38 μm, respectively, when shearing is applied for 10 min. However, the reverse seepage velocity and absolute permeability in the bed decrease to various extents after shearing. Meanwhile, the maximum flow rate reaches 1.537 μm/s and the absolute permeability increases by 14.16%. Shearing alters the formation process and the pore structure of the seepage channel. Isolated pores connect to the surrounding flocs to form branch channels, which then become the main seepage channel and create the dominant water-seepage flow channel.