Understanding the effects of cropping practices on soil pore characteristics is important for determining soil productivity and ecosystem services. Objectives of the study were to compare differences in computed tomography (CT) measured soil pore parameters (number of macropores, macroporosity, area of the largest pore, circularity and fractal dimension) among cover crops (CC), no-cover crops (NCC), and biofuel crops [Miscanthus (M): Miscanthus x giganteus and switchgrass (SG): Panicum virgatum] and examine relationships between CT-measured pore parameters and soil hydraulic and thermal properties. Cover crops were Cereal rye (Secale cereale L.), Hairy vetch (Vicia villosa) and Austrian winter pea (Pisum sativum subsp. arvense). Three replicates each of undisturbed soil cores were collected at two soil depths (0–10 and 10–20 cm) from each treatment using plexiglass cores measuring 76.2 mm diameter by 76.2 mm long. Ten scan images from each core were acquired using an X-ray CT scanner with 0.19 by 0.19 mm pixel resolution with 0.5 mm slice thickness and analyzed with Image-J. Soil under CC, NCC, M, and SG on average had 21, 14, 17, and 12 macropores on a 2500 mm² area across all the depths. Soil under miscanthus had significantly greater macroporosity (0.049 m² m^− 2) and area for the largest pore (89.70 mm²) than other treatments. The cover crop treatment had approximately 50%, 28%, and 75% greater number of macropores than NCC, M, and SG treatments. Bulk density (D_b) of soil was 13% lower in M than the NCC. Saturated hydraulic conductivity (K_sat) values were positively correlated with most CT-measured pore parameters. In contrast, D_b was negatively correlated with most CT-measured pore parameters (circularity and fractal dimension were positively correlated). While the circularity values were correlated positively with D_b and thermal conductivity (λ), the fractal dimension was correlated positively with volumetric heat capacity (C_v). The study illustrates that M and CC treatments can improve soil pore parameters.