Due to the mechanism of microstructural transition, high-strength low-carbon alloy steel gears exhibit high strength and surface hardness after Carburizing-Quenching-Tempering (CQT) combined heat treatment, while maintaining good toughness in the core. The carbon potential gradient and the precipitation of carbides are the main factors affecting the final microstructure, yet there is a shortage of related research. To address this gap, this study developed a multi-physics coupled model considering the impact of carbon content to simulate microstructural transformation. Using finite element analysis, we simulated the microstructural evolution during the CQT heat treatment of 20MnCr5 bevel gear. By comparing the simulation results with the calculations from the commercial heat treatment software DANTE®, the accuracy of this model in predicting microstructural distribution and hardness has been validated. Furthermore, the study established a carbide precipitation kinetics model that takes into account the influence of grain size, to investigate the precipitation behavior of carbides within the matrix during the tempering stage. The cellular automaton method was applied to demonstrate the evolution process of the quenched microstructure during tempering. The study shows that during tempering, carbides primarily precipitate in areas with higher carbon content, preferentially at the boundaries of fine grains with a high density of lattice defects. As the carbon content increases, the number density of precipitates rises, while their average radius decreases. The reduction in matrix supersaturation due to carbide precipitation is one of the causes for the reduction of tooth surface hardness during tempering. The model constructed in this study provides a new perspective for understanding the laws governing material microstructural evolution and offers a solid theoretical foundation for the study of stress and deformation during the heat treatment process.