Land subsidence has caused serious geological damage in many countries, including China. Soil pore number, size, shape, and pore size distribution affect soil deformation and thus land subsidence. Quantification of complex pore structures in different soil types and at various soil depths, however, remains cumbersome. The objective of this study was to quantify pore characteristics of three different soil types using computed tomography (CT) technique, investigate the effects of soil depth, examine the relationships between various parameters, and preliminarily determine the pore deformation pattern. Undisturbed soil samples (70 mm diameter × 50 mm height) of clay, silt, and silty clay soils were collected from two 300-m-deep engineering geological boreholes on both sides of the Xi’an D7 ground fissure. One hundred CT images were acquired for each soil sample. Soil pore characteristics and morphological parameters, including porosity, macroporosity, coarse mesoporosity, microporosity, number of pores, number of macropores (diameter > 1000 μm), number of coarse mesopores (diameter 200–1000 μm), number of micropores (diameter < 200 μm), circularity, structure model index, degree of anisotropy, and the Euler number, were analyzed. Micropores were generally regularly shaped and the main contributors to the total number of pores, whereas macropores were mostly elongated and contributed to total porosity. With increasing depth, the most noticeable changes appeared in silt soil and the least noticeable in clay soil. The alternate pore deformation pattern was significant in silt and silty clay soils. Soil depth significantly influenced all soil pore parameters, whereas soil type significantly affected the remaining parameters, except circularity and degree of anisotropy. The elongated macropores in silt and silty clay soils favor land subsidence in the Xi’an area. The present results can help optimize the groundwater exploitation layer, reducing soil compaction and land subsidence in this area.