Shale gas is a prospective cleaner energy resource and the exploration and development of shale gas has made breakthroughs in many countries. Structure deformation is one of the main controlling factors of shale gas accumulation and enrichment in complex tectonic areas in southern China. In order to estimate the shale gas capacity of structurally deformed shale reservoirs, it is necessary to understand the systematic evolution of organic pores in the process of structural deformation. In particular, as the main storage space of high-over-mature marine shale reservoirs, the organic matter pore system directly affects the occurrence and migration of shale gas; however, there is a lack of systematic research on the fractal characteristics and deformation mechanism of organic pores under the background of different tectonic stresses. Therefore, to clarify the above issues, modular automated processing system (MAPS) scanning, low-pressure gas adsorption, quantitative evaluation of minerals by scanning (QEMSCAN), and focused ion beam scanning electron microscopy (FIB-SEM) were performed and interpreted with fractal and morphology analyses to investigate the deformation mechanisms and structure of organic pores from different tectonic units in Silurian Longmaxi shale. Results showed that in stress concentration areas such as around veins or high-angle fractures, the organic pore length-width ratio and the fractal dimension are higher, indicating that the pore is more obviously modified by stress. Under different tectonic backgrounds, the shale reservoir in Weiyuan suffered severe denudation and stronger tectonic compression during burial, which means that the organic pores are dominated by long strip pores and slit-shaped pores with high fractal dimension, while the pressure coefficient in Luzhou is high and the structural compression is weak, resulting in suborbicular pores and ink bottle pores with low fractal dimension. The porosity and permeability of different forms of organic pores are also obviously different; the connectivity of honeycomb pores with the smallest fractal dimension is the worst, that of suborbicular organic pores is medium, and that of long strip organic pores with the highest fractal dimension is the best. This study provides more mechanism discussion and case analysis for the microscopic heterogeneity of organic pores in shale reservoirs and also provides a new analysis perspective for the mechanism of shale gas productivity differences in different stress–strain environments.