The vast majority of oil and gas reserves are trapped in fractured carbonate reservoirs. Most carbonate reservoirs are naturally fractured, with fractures ranging from millimeter- to kilometer scales. These fractures create complex flow behaviors which impact reservoir characterization, production performance, and eventually, total recovery. Bridging the gaps from plug to near-wellbore to field scales is a persisting challenge, which requires a fundamental understanding of flow behaviors at the plug scale. This dissertation aims to advance the fundamental flow mechanisms in fractured rocks at the plug scale, including fracture roughness, rock mechanics, matrix-fracture interaction, and non-Darcy effect, further deepen the understanding of the governing upscaling parameters, and eventually develop a fit-for-purpose upscaling tool that is applicable at the field scale.