Abstract Carbonate hydraulic behavior emerges from flow through pore structures spanning resolvable macropores and sub‐resolution microporous regions, yet the effects of microporosity level and heterogeneity remain poorly understood. We develop and validate a CUDA‐accelerated lattice Boltzmann model that unifies pore‐resolved and continuum flow. Simulations show that low‐velocity microporous regions substantially contribute to bulk flow by activating connections between macropores. Across three carbonate samples, permeability increases nonlinearly with microporosity, with reference permeabilities spanning over two orders of magnitude. Moreover, at fixed bulk porosity, amplifying the observed phase‐wise contrast increases permeability, while spatial permutation controls reveal a dominant contribution from the original spatial organization. Three‐dimensional spatial and pressure‐gradient analyses further indicate that high‐microporosity phases preferentially adjacent to macropores become increasingly conductive as heterogeneity increases, reducing local flow resistance. These results show how naturally organized microporosity controls hydraulic behavior and bulk permeability in multiscale geological porous media.