Southern China is affected by multi-stage tectonic activities, with strong fold deformation, complex fault systems and poor shale gas preservation conditions. Here, we used shale samples from the lower Silurian Longmaxi shale in the complex tectonic area of Southern China, to study the relationship between differential structural deformation, and pore structure and adsorption capacity. According to the deformation mechanism of the shale, it is further divided into brittle-slip rheological deformation (BD) and ductile-slip rheological deformation (DD). The results show that all micro-fractures can be observed under scanning electron microscopy in deformed shale samples, but in shale samples with different types of rheological deformation, the micro-fractures have large differences in scale, fracture length and lateral connectivity. The micro-fractures developed in DD shales are small in scale and short in fracture length, but have strong local connectivity. In contrast, brittle minerals are more developed in BD shales, and interlayer shearing has formed micro-fractures with large fracture length and good lateral connectivity, which is beneficial for later fracturing. In these two types of deformed shales, pores in organic matter are rare, and sporadic organic pores have small pore size and poor connectivity. The total pore volume (1.8–2.4 × 10−2 cm3 g–1) of BD shale samples is higher than that of DD shale samples (0.8–1.6 × 10−2 cm3 g–1). There is a positive correlation between total pore volume and quartz content. In addition, the specific surface area (12–18 m2 g–1) of DD shale samples is larger than that of BD shale samples (6–12 m2 g–1).