With estimated shale gas resources greater than those of US and Canada combined, China has been embarking on an ambitious shale development program. However, nearly 30 years of American experience in shale hydrocarbon exploration and production indicates a low total recovery of shale gas at 12 %–30 % and tight oil at 5 %–10 %. One of the main barriers to sustainable development of shale resources, namely the pore structure (geometry and connectivity) of the nanopores for storing and transporting hydrocarbons, is rarely investigated. In this study, we collected samples from a variety of leading hydrocarbon-producing shale formations in US and China. These formations have different ages and geologic characteristics (e.g., porosity, permeability, mineralogy, total organic content, and thermal maturation). We studied their pore structure characteristics, imbibition and saturated diffusion, edge-accessible porosity, and wettability with four complementary tests: mercury intrusion porosimetry, fluid and tracer imbibition into initially dry shale, tracer diffusion into fluid-saturated shale, and high-pressure Wood’s metal intrusion followed with imaging and elemental mapping. The imbibition and diffusion tests use tracer-bearing wettability fluids (API brine or n-decane) to examine the association of tracers with mineral or organic matter phases, using a sensitive and micro-scale elemental laser ablation ICP-MS mapping technique. For two molecular tracers in n-decane fluid with the estimated sizes of 1.39 nm 9 0.29 nm 9 0.18 nm for 1-iododecane and 1.27 nm 9 0.92 nm 9 0.78 nm for trichlorooxobis (triphenylphosphine) rhenium, much less penetration was observed for larger molecules of organic rhenium in shales with median pore-throat sizes of several nanometers. This indicates the probable entanglement of sub-nano-sized molecules in shales with nano-sized pore-throats. Overall findings from the above innovative approaches indicate the limited accessibility (several millimeters from sample edge) and connectivity of tortuous nanopore spaces in shales with spatial wettability, which could lead to the low overall hydrocarbon recovery because of the limited fracture– matrix connection and migration of hydrocarbon molecules from the shale matrix to the stimulated fracture network.