Sedimentary carbonate rocks are one of the principal porous structures in natural reservoirs of hydrocarbons such as crude oil and natural gas. Efficient hydrocarbon recovery requires an understanding of the carbonate pore structure, but the nature of sedimentary carbonate rock formation and the toughness of the material make proper analysis difficult. In this study, a novel preparation method was used on a dolomitic carbonate sample, and selected regions were then serially sectioned and imaged by focused ion beam–scanning electron microscopy. The resulting series of images were used to construct detailed three-dimensional representations of the microscopic pore spaces and analyze them quantitatively. We show for the first time the presence of nanometer-scale pores (50–300 nm) inside the solid dolomite matrix. We also show the degree of connectivity of these pores with micron-scale pores (2–5 μm) that were observed to further link with bulk pores outside the matrix.