This study investigates the complex relationship between organic matter (OM), tectonic deformation, and pore structure development in Eocene Bhainskati shale within the Lesser Himalayan foreland basin, Nepal, to assess its implications for shale gas accumulation and preservation. We hypothesize that tectonic deformation and variations in organic matter have a significant impact on pore size distribution, connectivity, and gas retention, thereby influencing shale gas potential. We characterized pore types and quantified pore size distributions using scanning electron microscopy (SEM), mercury intrusion capillary pressure (MICP) techniques, and low-pressure gas adsorption methods. Our findings indicate a predominance of mesopores (1–10 nm range, with a notable peak at 4 nm), suggesting substantial contributions to surface area from micropores and fine mesopores. Thermal maturity negatively impacts porosity and surface area. At the same time, tectonic activity enhances microfracture development, increasing permeability and gas transport, particularly in the Surkhet area, which exhibits higher pore volume and specific surface area than the Tansen area. Tectonic forces shift the shale from brittle to ductile behavior, altering pore connectivity. Himalayan tectonic forces significantly influence shale structure, pore sizes, gas preservation, and migration, enhancing gas adsorption by increasing surface area but posing challenges due to potential gas escape along faults and folds. Understanding the impact of tectonic activity on shale deformation in similar basins within the Himalayas and the adjacent region is vital for assessing shale gas potential and optimizing exploration strategies in tectonically active Nepal Himalayan regions. This study highlights the dual role of tectonics in both promoting and complicating the formation, accumulation, and preservation of shale gas reservoirs, offering critical insights for future exploration efforts.