The chemical structure characteristics of organic matter (OM) in marine-continental transitional (MCT) shales and the controls on shale gas accumulation were revealed through analysis of Raman spectroscopy, infrared spectroscopy, X-ray diffraction (XRD), transmission electron microscopy (TEM), and CO2 adsorption tests on the Lower Permian Shan-2 shale OM samples from the eastern margin of the Ordos Basin. Organic matter in the high-mature shale is enriched in aromatic groups, with a noticeable condensation and polymerization of the chemical structure after similar to 3.0 %R-mc (Raman-based R-o). As %R-mc increases from 2.30 to 3.42, the position of the (002) peak from the stacking of aromatic layers increases from 25.15 degrees to 25.88 degrees in XRD spectra, the spacing between aromatic layers (d(002)) decreases from 0.3540 nm to 0.3444 nm, the calculated graphitization degree (level of OM transforming into graphite) gradually increases, and the carbon layers in the OM evolve from a chaotic shape to a better-oriented state in TEM images, directly indicating an elevated graphitized level. Release of heteroatoms from OM results in reduced average lateral size (L-a) and stacking height (L-c) of the aromatic layer, reaching minimum values at similar to 3.0 to 3.2 %R-mc. The stacking of aromatic layers forms some organic micropores, as evidenced by similar micropore size distribution between OM and bulk shale samples, possibly favoring methane accumulation. These findings provide new insights into the factors that affect the gas accumulation characteristics in MCT shales.