Kerogen maturity is an important indicator for evaluating source rocks. We propose a kerogen maturity index (molecule-maturity index, MMI) based on the changes in the molecular structure of organic matter during thermal evolution. The MMI has a positive correlation with vitrinite reflectance. Molecular dynamics simulations indicate that the weight loss is with a positive linear correlation with the MMI, demonstrating the ability of the index to reflect the hydrocarbon generation of organic matter. In addition, a new conversion is introduced by the MMI to analyze the kinetics of kerogen thermal evolution. The activation energy is expressed as a continuous function of the MMI linking by the new conversion. The activation energy was calculated at the isoconversional points of previous conversion, which was not defined as a continuous function before. A linear relationship between the activation energy of kerogen is observed, and a new chemical kinetic model of kerogen thermal maturity is established based on the MMI (kinetic model of the maturity evolution, MEKM). The MEKM equation has a simple form and is convenient for engineering applications. Our findings provide insights into the kinetics of kerogen thermal maturation and guide the choice of temperature and time for artificial maturity.