The Lower Paleozoic marine shale in southern China has undergone several strong tectonic transformations in an extensive region outside the Sichuan Basin. Although some shale strata underwent strong deformation, they still contain a significant amount of shale gas. The gas preservation mechanism in the strongly deformed shale has become the focus of attention. In this paper, the Lower Cambrian gas-bearing shale samples with a strong deformation taken from an exploration well in northern Chongqing, China, were investigated on their pore types and structure, with the aim to reveal the reason for the gas preservation. The pore types of the Lower Cambrian shale are dominated by microfractures and interparticle (interP) pores occurring mainly between clay minerals and between organic matter (OM) and clay minerals, while pores within OM that can be observed by FE-SEM (field emission-scanning electron microscopy) are rare. The shale has a low porosity, with an average of 1.56%, which is mainly controlled by the clay mineral content. The adsorption experiments of low pressure N2 (LPNA) and CO2 (LPCA) indicate that the shale is rich in micropores and small mesopores (<2–3 nm) provided mainly by OM, but mesopores with a size range of 3–50 nm are underdeveloped. The shale, as revealed by LPNA data, has dominant slit-like or plate-like pores and an obvious low-pressure hysteresis (LPH), indicating a low gas diffusion. The deformed shale samples with a removal of OM by oxidation and their isolated kerogen further indicate that the LPH is completely related to OM, without any relationship with minerals, while an undeformed shale sample, taken from another well for a comparison, has no obvious LPH for both of its OM-removed sample and kerogen. Based on a comprehensive analysis of the relative data, it is suggested that the nanopores related to OM and clay minerals in the shale were significantly altered owing to the deformation, with a result of the pores being squeezed into the slit-like shape and converted into micropores. This extraordinary pore structure of the shale formed during the deformation process should be the main preservation mechanism of shale gas.