We applied three-dimensional X-ray microtomography to image a capillary drainage process (0–1,000 kPa) in a cm-scale heterogeneous laminated sandstone containing three distinct regions with different pore sizes to study the capillary pressure. We used differential imaging to distinguish solid, macropore, and five levels of subresolution pore phases associated with each region. The brine saturation distribution was computed based on average CT values. The nonwetting phase displaced the wetting phase in order of pore size and connectivity. The drainage capillary pressure in the highly heterogeneous rock was dependent on the capillary pressures in the individual regions as well as distance to the boundary between regions. The complex capillary pressure distribution has important implications for accurate water saturation estimation, gas and/or oil migration and the capillary rise of water in heterogeneous aquifers.