The hierarchical organization of aggregates in soil is responsible for the presence of inter and intra-aggregate pores. This research aimed to investigate effects of soil surface liming, considering lime rates of 0, 10 and 15 t ha−1, on the intra-aggregate porous system of soil aggregates with equivalent diameters of 2–4 and 1–2 mm, from 0 to 10 (A) and 10 to 20 cm (B) soil layers. These aggregates were selected by the wet sieving method carried out for determination of the mean weight diameter. Synchrotron-based computed microtomography (μCT) of aggregates was analyzed in terms of porosity, connectivity, tortuosity, and fractal dimension. Additionally, X-ray fluorescence was used to evaluate the elemental composition of the soil aggregates. All liming effects were concentrated at layer A, where calcium percentage was elevated in aggregates from 1–2 mm class as compared to those from 2–4 mm class. Accordingly, the physical parameters studied were generally more affected in the case of smaller aggregates (1–2 mm). Liming decreased total porosity, increased tortuosity of pores, and decreased fractal dimension for 1–2 mm aggregates, which was in line with the fact that larger pores were replaced by smaller ones in 1–2 mm aggregates, as found via both quantitative and qualitative analyses. On the other hand, liming did not affect pore connectivity under any of the circumstances.