Quantitative characterization of the geo-mechanical properties of shale and organic matter (OM) holds paramount significance in the assessment of shale gas reserves and the design of hydraulic fracturing. However, the mechanical evolution processes during shale hydrocarbon generation and its influencing factors have received limited attention. This study examines the changes in shale mechanical properties during pyrolysis at high temperatures (415–600 °C) and high pressure (50–125 MPa) for mature to over-mature stages. The nanoindentation and in-situ AFM-QNM analysis are utilized to characterize the changes in mechanical properties during evolution. Subsequently, gas adsorption, Fourier Transform infrared spectroscopy (FTIR), and laser Raman spectroscopy (Raman) are used to investigate the factors influencing the mechanical properties of shale and the associated OM, and establish a model for the evolution of the mechanical properties. The results demonstrate that with increasing maturity, the overall Young's modulus of the bulk shale gradually increases from 42.8 GPa to 58.4 GPa for the temperature increment from 415 °C to 600 °C. During the thermal maturation process, the mesopore structure and quartz content of the shale significantly influence its mechanical properties. Young's modulus of OM shows an S-shaped trend, with variations in the micromechanical properties of OM corresponding to stages of hydrocarbon generation. In particular, two peaks of Young's modulus increase are observed during the mature and over-mature stages. In the mature stage, the aromatization of the kerogen leads to substantial detachment of aliphatic side chains and oxygenated functional groups, resulting in a higher degree of aromatization. This reduces the kerogen spacing and consequently increases the Young's modulus. In the over-matured stage, the process of aromatics condensation leads to the orientation and arrangement of aromatic rings, reducing the number of key site vacancies and crystal defects, thereby forming large aromatic clusters and significantly increasing the graphite-like structure. This study will facilitate the analysis of shale matrix deformation mechanisms at the microscale, providing a fundamental theoretical and scientific basis for shale fracturing design, exploration, and development.