【Objective】The plough layer of fluvo-aquic soil is shallow, while the subsoil is hard and compacted, exhibiting significant structural obstacles. Tillage and straw return are key measures for improving soil structure; however, the mechanism through which the combination of these agricultural practices affects soil structure remains elusive. 【Method】Undisturbed soil columns (20 cm height × 10 cm diameter) were collected from a fluvo-aquic soil experimental site at the Shangqiu Station of the national field Agro-ecosystem experimental network. The samples represented plots under rotary tillage (RT), deep ploughing (DP), and biennial deep ploughing (BDP), with and without straw returning. X-ray computed tomography (XCT) scanning, ImageJ software, and machine learning techniques were employed to perform three-dimensional reconstruction and visualization of the soil pore structure. The effects of different tillage methods and straw treatments on macroporosity, pore size distribution, pore morphology, network characteristics, saturated hydraulic conductivity, and air permeability were quantitatively analyzed. 【Result】Without straw return, deep ploughing and biennial deep ploughing increased macroporosity by 31.5% and 5.7%, respectively, compared to rotary tillage. With straw return, deep ploughing significantly increased macroporosity by 92.9% and 68.4% compared to rotary tillage and biennial deep ploughing, respectively (P < 0.05). Furthermore, the hydraulic radius increased significantly by 53.8% and 42.9%, respectively. Compactness increased significantly by 1.5 and 2.9 times, and global connectivity increased significantly by 12 times. Both saturated hydraulic conductivity and air conductivity were significantly enhanced (P < 0.05). 【Conclusion】 Deep ploughing increased the hydraulic radius of soil pores, improved connectivity, and enhanced pore network complexity, thereby constructing a relatively favorable soil pore morphology and network structure. This enhanced hydraulic and air conductivity, significantly reducing the structural obstacles in fluvo-aquic soil.