Sewage irrigation has a strong influence on the physical, chemical, and biological properties of soil. However, the effects of sewage irrigation on the pore characteristics of soil are not well understood. This study compares the effects of sewage irrigation and groundwater irrigation on computed tomography (CT)-measured pore parameters and examines the relationships between CT-measured pore parameters and soil physicochemical and microbial properties. Intact soil cores were collected from S1 irrigated with sewage for 25 years, S2 irrigated with sewage for 52 years, and CK irrigated with groundwater. Various soil pore characteristics were determined, including the total pore number, macropore number (>1 mm diam.), coarse mesopore number (0.264–1 mm diam.), total porosity, macroporosity, coarse mesoporosity, and circularity. The results indicated that sewage irrigation significantly affected soil pore number and porosity. Compared with S1 and S2, CK exhibited a higher average total pore number (91), macropore number (40), coarse mesopore number (51), total porosity (2.08%), macroporosity (1.90%), and coarse mesoporosity (0.18%) throughout the 50–350 mm layer. At depths of 200–350 mm, S2 exhibited the lowest average total pore number (33), macropore number (13), coarse mesopore number (21), total porosity (0.42%), macroporosity (0.35%), and coarse mesoporosity (0.07%) among the three sites. In addition, the average pore numbers and porosity at depths of 200–350 mm decreased with increasing sewage irrigation time. There were significant positive correlations between pore features (including pore numbers and porosity) and soil properties (phosphorus content and fungi numbers). Our results suggest that decreased macropore numbers and macroporosity in the sewage-irrigated farmland may strongly intensify the accumulation of metals and nutrients in the upper layer. The findings of this study are useful for understanding the negative effects of sewage irrigation on soil pore structure and are critical for developing sustainable strategies in agriculture.