Petrophysical characterization and understanding of pore systems and producibility in unconventional reservoirs remains challenging when evaluating reservoir potential. This study’s main objective is to identify and evaluate the controls on petrophysical rock types in unconventional low porosity, low permeability carbonate reservoirs in Mississippian-aged rocks of the southern Midcontinent. Representative samples selected from cores in the study area are calcareous siltstones and grain-rich packstones to grainstones. Rock fabric, pore types, and pore structure of 23 samples were investigated using multiscale image analysis of optical micrographs and scanning electron microscope (SEM) mosaics. Petrographic observations and quantified pore parameters were correlated with nuclear magnetic resonance (NMR) plug measurements of transverse relaxation times (T2), pore size distribution, and porosity. Results indicate that pore structure, permeability, and NMR response are closely linked to the dominant pore types, pore sizes, and mineralogy, which are distinctive for specific rocks—allowing for petrophysical rock type (PRT) grouping. NMR signature geometry is distinct in each of these rock type groups. Complex mixed mineralogies in these rocks homogenizes porosity and permeability relationships among rocks of different depositional facies, making it difficult to define clear-cut correlative relationships between pore architecture, rock fabric, and petrophysical response. Petrographic assessment indicates that the primary cause of pore-scale heterogeneity and varying petrophysical response is related to postdepositional diagenesis, such as silicification, cementation, dissolution, and mineralization along pores and pore throats, which produce complicated pore systems and affects matrix permeability. These observations confirm that incorporating geologic information such as mineralogy, diagenesis, and pore types/pore architecture into rock typing workflows in carbonate mudrock reservoirs is critical to understanding petrophysical response. Additionally, the distinct geometries in each petrophysical rock type group establishes the viability of using NMR as a rock typing tool based on the correlative relationships between NMR response, pore types, and facies.