Until recently, the characteristics of nano-microscale structures in the naturally deformed, overmature, marine shales were poorly known. Thermally overmature Lujiaping shales in the complex tectonic area of the northeast part of the upper Yangtze area, China have experienced strong tectonic deformation and are considered as potentially important strata for shale gas exploration. Naturally deformed samples from the main source rocks are selected from the Lower Cambrian Lujiaping Formation in the Dabashan Thrust-fold Belt to investigate nanometer- to micrometer-sized structures. A combination of scanning electron microscope (SEM), low-pressure nitrogen adsorption (LPNA), and low-field nuclear magnetic resonance (NMR) suggests that the pore types are dominantly fracture-related pores with a lesser abundance of mineral-hosted pores. These two pore types account for the 90% of total pore space. Organic matter (OM)-hosted pores are rare and make up a small part of the pore systems (less than 10%) due to high thermal maturity and intensive tectonic compression. Overall, the Lujiaping deformed, overmature samples have abundant nanometer- to micrometer-sized inorganic pores. High-resolution SEM images provide direct evidence of the formation of nano- and microsized structures such as OM–clay aggregates and silica nanograins. OM–clay aggregates are commonly observed in samples, which also exhibit abundant open microfractures and interparticle pores. Quartz can occur as silica nanograins and botryoids typically 20–100 nm in size, which may influence porosity through the creation or occupying interparticle pore space.