During diagenesis, the transformation of unconsolidated sediments into a sandstone is usually accompanied by compaction, water expulsion, cementation and dissolution, which fundamentally control the extent, connectivity and complexity of the pore structure in sandstone. As the pore structure is intimately related to fluid flow in porous media, it is of great importance to characterize the pore structure of a hydrocarbon-bearing sandstone in a comprehensive way. Although conventional petrophysical methods such as mercury injection porosimetry, low-pressure nitrogen or carbon dioxide adsorption are widely used to characterize the pore structure of rocks, these evaluations are based on idealized pore geometry assumptions, and the results lack direct information on the pore geometry, connectivity and tortuosity of pore channels. In view of the problems, X-ray micro-CT was combined with ImageJ software (version 1.8.0) to quantitatively characterize the pore structure of Berea Sandstone. Based on its powerful image processing function, a series of treatments such as contrast enhancement, noise reduction and threshold segmentation, were first carried out on the micro-CT images of the sandstone via ImageJ. Pores with sizes down to 2.25 μm were accurately identified. Geometric parameters such as pore area, perimeter and circularity could thus be extracted from the segmented pores. According to our evaluations, pores identified in this study are mostly in the range of 30–180 μm and can be classified into irregular, high-circularity and slit-shaped pores. An irregular pore is the most abundant type, with an area fraction of 72.74%. The average porosity obtained in the image analysis was 19.10%, which is fairly close to the experimental result determined by a helium pycnometer on the same sample. According to the functional relationship between tortuosity and permeability, the tortuosity values of the pore network were estimated to be in the range of 4–6 to match the laboratory permeability data.