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Shale deformation is crucial in various geological processes. To investigate the effect of deformation on pore characteristics for highly compacted shale, the macro tectonic strain and micro pore structure were analyzed in the deeply buried Wufeng–Longmaxi shale of the Eastern Fold Belt of the Sichuan Basin. Despite similarities in their X-ray diffraction mineral compositions, significant differences in pore properties were observed between the shale samples from weak and strong curved synclines. Pore shapes identified from scanning electron microscopy and the covariation between total organic carbon (TOC) content and porosity suggest that organic pores predominantly contribute to total porosity. However, samples from weak-curved synclines exhibit porosities ∼2% higher than samples from strong-curved synclines, even with similar TOC contents. Compared to the weak-curved syncline samples, the strong-curved syncline samples show a transformation in organic pore morphology from spherical to elliptical with an increasing aspect ratio and reduced dominant pore size from 1–1000 nm to 1–100 nm due to pore collapse in the organic matrix. The porosities simulated using a syncline bending ductile strain model align well with the measured porosities, indicating that the porosity changes were induced by heterogeneous ductile strain during detachment folding. Strain heterogeneity also triggered tectonic stress heterogeneity, causing clockwise rotation of the principal stress orientation from weak to strong curved synclines. This study improves our understanding of the variations in pore system with syncline deformation strain, providing a theoretical basis for subsequent shale hydrocarbon exploration and resource assessment in complex tectonic zones.