Organic rich sedimentary rocks of the Late Cretaceous Muwaqqar Formation from the Lajjun outcrop in the Lajjun Sub-basin, Western Central Jordan were geochemically analyzed. This study integrates kerogen microscopy of the isolated kerogen from 10 oil shale samples with a new finding from unconventional geochemical methods [i.e., ultimate elemental (CHNS), fourier transform infrared spectroscopy and pyrolysis–gas chromatography (Py–GC)] to decipher the molecular structure of the analyzed isolated kerogen fraction and evaluate the kerogen composition and characteristics. The optical kerogen microscopy shows that the isolated kerogen from the studied oil shales is originated from marine assemblages [i.e., algae, bituminite and fluorescence amorphous organic matter] with minor amounts of plant origin organic matter (i.e., spores). This finding suggests that the studied kerogen is hydrogen-rich kerogen, and has the potential to generate high paraffinic oil with low wax content. The dominance of such hydrogen-rich kerogen (mainly Type II) was confirmed from the multi-geochemical ratios, including high hydrogen/carbon atomic of more than 1.30 and high A-factor of more than 0.60. This claim agrees with the molecular structure of the kerogen derived from Py–GC results, which suggest that the studied kerogen is mainly Type II-S kerogen exhibiting the possibility of producing high sulphur oils during earlier stages of diagenesis, according to bulk kinetic modeling. The kinetic models of the isolated kerogen fraction suggest that the kerogen conversion, in coincidence with a vitrinite reflectance range of 0.55–0.60%, commenced at considerably lower temperature value ranges between 100 and 106 °C, which have produced oils during the early stage of oil generation. The kinetic models also suggest that the commercial amounts of oil can generate by kerogen conversion of up to 50% during the peak stage of oil window (0.71–0.83%) at relatively low geological temperature values in the range of 122–138 °C. Therefore, further development of the Muwaqqar oil shale successions is highly approved in the shallowly buried stratigraphic succession in the Lajjun Sub-basin, Western Central Jordan.