Carbonate microporosity can vary significantly across depositional lithofacies and cycles, owing primarily to the high degree of heterogeneity in their pore sizes, pore throat radius, geometry, and connectivity. This is further compounded by the complex diagenetic alterations during various stages of burial. In addition, the presence of micropores, which are abundant in carbonate rocks, but not visible using conventional techniques, is challenging to characterize. To address this issue, our study focused on the Middle Jurassic Tuwaiq Mountain Formation (TMF) due to its importance as an analogue to subsurface conventional and unconventional reservoirs. Here, we utilized eight samples and performed pore network modeling to quantify microporosity distribution and connectivity from high-resolution microcomputed tomography images of different microfacies (MF) in the TMF from both mud- and grain-dominated facies. These results were then validated with petrographic, SEM images, and porosity-permeability measurements. Our study revealed that, in the high-energy, grain-supported microfacies of the shallow lagoon depositional cycle, micropores dominated by interparticle and microvug types were abundant and well-connected, with mean pore and throat sizes of 7 and 4 μm. Conversely, micropores within the low-energy mud-dominated microfacies of the deep lagoon depositional cycle dominated by intraparticle and intercrystalline types were isolated and rarely connected, even at the microscale (1-4 μm in diameter, with an average of 2 μm). This result suggests that pore connectivity at the microscale is not always related to matrix porosity, and the pore connectivity is present in submicron scale, which goes against common concepts in unconventional carbonate reservoirs. Furthermore, our observations indicate that primary depositional processes play a major role in controlling the distribution and connectivity of the Tuwaiq Mountain Formation's microporosity, while diagenetic processes only have minor controls. Our study emphasizes the importance of characterizing microporosity and its connectivity in heterogeneous carbonate rocks, which may reduce the uncertainty in exploring the properties of complex carbonate reservoirs worldwide.