The Cretaceous Late Cenomanian-Early Turonian Mishrif Formation carbonates in the Mesopotamian Basin are characterized by complex pore systems, resulting in strong reservoir quality heterogeneity. Major factors that constitute the complexity of pore structure are types, geometries, and topologies of pores and pore-throats. These factors and the effect of pore structure on reservoir quality were investigated by integration of thin sections, petrographic image analyses, porosity, permeability, and mercury injection capillary pressure measurements. Eight matrix-related and three matrix-unrelated pore types, which are dominated by secondary pores, are identified in the Mishrif carbonates. Pore sizes range from a few microns to more than 1 cm and vary greatly both in the same and in different pore types. Pore shapes range from better circularity and simple boundaries to irregular complex boundaries and similar for the same pore type. Porethroat radii (PTR) range from 3 nm to 124 μm, and micro pore-throats occur in all carbonates in different proportions. Pore-throat systems show strong heterogeneity and are classified into six classes based on their size distribution characteristics. Carbonate porosity is not solely correlated with pore sizes because pore abundance is another independent factor to determine porosity. Permeability is controlled by PTR rather than pore sizes, and R 40 (PTR corresponding to the 40th percentile of mercury saturation) is the most correlated PTR to permeability. There is no apparent correlation between pore size and PTR except for the interparticle pores. Both pore sizes and PTR distributions can reflect reservoir microscopic heterogeneity due to their positive correlations for all pore types other than micropores (pore diameter less than 30 μm).