Abstract Tectonism caused strong deformation of the Wufeng-Longmaxi Formation in the periphery of the Sichuan Basin, which affected the pore-fracture of the organic-rich shale and migration of shale gas. Samples of structurally deformed shale from the anticline and detachment structure and undeformed shale were collected in the Northeast Chongqing area, China. The investigations of shale structural deformation and its pore-fracture system were performed using optical microscopy, field emission scanning electron microscopy (FE-SEM), low-pressure gas adsorption (LP-GA), and small-angle X-ray scattering (SAXS). The research shows that deformed samples with curved beddings and friction mirrors on the macro level, as well as the microscopically curved organic matter (OM) bands and OM folds, indicate the significant structural transformation and predominantly ductile deformation. The micro-fractures in deformed samples are more developed with different combinations in two geological structures, showing brittle deformation. Compared with undeformed samples, the number of OM pores in deformed samples is reduced significantly, while the interparticle (interP) pores, intraparticle (intraP) pores, and micro-channels are more developed. The connected pore size distribution (PSD) of all samples is mainly from 0.3 nm to 10 nm. The pore volume (PV) of micropore in the deformed samples is between 0.100–0.500 cm3/100 g, and the specific surface area (SSA) is in the range of 2.175–13.554 m2/g. Undeformed samples have a larger PV and SSA than the deformed samples. TOC and the structural deformation control the structure of connected pore, and their PV and SSA are positively correlated with TOC content. Fractal dimension reveals that the surface of connected and closed pore (pore size 3.81–95.34 nm) becomes more complex, and the distribution of small pore (pore size 1.25–3.81 nm) becomes more uniform under the structural deformation of the shale. As the degree of shale deformation increases, the mesopore and macropore volume of connected pores decrease significantly, while the strongly structural deformation of samples results in a substantial increase in micropore volume and SSA. Besides, the PV of both closed and connected pores tends to decrease and the average pore size increases linearly. Furthermore, the shale deformation result in a weakening of the methane adsorption capacity. Shale gas can migrate through the fracture network to the central zone of the detachment structure or the core of the anticline, which has a significant effect on shale gas enrichment and preservation.