Soil structure is modify when subjected to the agricultural process, i.e., a new spatial organization of the pores system is formed, with relation to the physical quality of it. Thus the aim of this work was to visualize and quantify, through X-ray CT scan, the pores distribution in an oxidic Latosol submitted to a conservation management system with different gypsum doses. Three random trenches were dug lengthwise along the plant row in a very clayey gibbsitic dystrophic Red Latosol, subjected to the following gypsum levels: G0: absence of gypsum; G7: 7 Mg ha-1 and G28: 28 Mg ha-1 of additional gypsum, applied to the surface of the plant row. Undisturbed soil samples were collected in plexiglass tubes at depths of 0.20-0.34, 0.80-0.94 and 1.50-1.64 m after six years of coffee cultivation for quantification of 3D pores obtained by X-ray CT scan. The spatial variability of the soil structure was evaluated by semivariograms generated by 3D images in grayscale. Distribution of the detectable pore diameter was conducted by data mining. Statistical analyzes employed packages 'geoR' to semivariogram and 'randomForest' for data mining in R language. A greater spatial continuity of the pores occurred in the G7 at the three depths. The combined effects of the management system promoted a greater spatial variability of the soil structure in the G28 treatment. Based on geostatistical analyses, it can be infer that the adoption of the system under study promoted changes in the pore network in all directions (X, Y and Z), however with better pores continuity in the vertical direction(Z).