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A comprehensive understanding of the key factors controlling kerogen pyrolysis is essential for elucidating hydrocarbon generation in saline lacustrine source rocks. In this study, reactive force field molecular dynamics (ReaxFF-MD) simulations were employed to systematically investigate the effects of the temperature, water content, and salinity on the reaction pathways and product distribution during the pyrolysis of type II kerogen. The results indicate that the temperature is the dominant factor governing pyrolysis kinetics and product evolution. With an increasing temperature, the cleavage of weak bonds within the kerogen backbone is markedly accelerated, driving the system to evolve from heavy intermediates toward light hydrocarbons and gaseous products. Water molecules deeply participate in the pyrolysis process through hydrogen-donor and hydrogen-transfer mechanisms, significantly promoting product lightening. This promotive effect strengthens with an increasing water content but gradually approaches saturation under high-water conditions (approximately 400–600 H2O molecules in this study), indicating an upper limit to the regulatory role of water in finite-scale kerogen pyrolysis systems. The introduction of salt ions exerts a pronounced nonlinear inhibitory effect on kerogen pyrolysis. Compared to water-only systems, increasing salinity significantly suppresses the generation of light hydrocarbons while favoring the retention of medium- to heavy-chain components. When the salt concentration exceeds approximately 0.3 mol/L (corresponding to 10–15 NaCl molecules), the regulatory effect on product distribution no longer intensifies. This behavior is likely attributable to the saturation of salt-induced perturbations to the microscopic structure of water. By integration of the molecular simulation results with previous experimental studies, a coupled “water promotion–salt inhibition” mechanism is proposed. Water molecules facilitate product lightening by acting as hydrogen donors and stabilizing free radicals, whereas salt ions disrupt the hydrogen-bond network of water and stabilize aromatic radicals, thereby enhancing condensation reactions and carbon residue formation. This study elucidates the synergistic effects of the temperature, water, and salinity on kerogen pyrolysis at the molecular scale, providing theoretical insights into hydrocarbon generation processes in saline lacustrine unconventional source rocks.