Based on the thermodynamic conversion mechanism and energy transition principle, the three-dimensional (3D) grain growth process of AZ31 magnesium alloy was simulated by using the improved cellular automata (CA) model of Metropolis algorithm, and the grain size and grain growth kinetics were analyzed statistically. The simulation results showed that CA model with the improved transformation rules was closer to the normal growth process of the actual 3D grain. In the simulation process, the total free energy of the system decreased, and the grain size presented normal distribution at different times. The ratio of grain diameter to average grain diameter (R/Rm) of 1.0 was the largest in grain distribution, which satisfied the minimum energy criterion of grain evolution. The analysis of grain growth kinetics showed that the 3D grain growth process follows the relationship between average grain size and time during grain evolution, and the grain growth index was 0.47941, which was much closed to the theoretical value of 0.5. The grain size variation of AZ31 magnesium alloy during heat preservation was studied by experiments, which further verified the reliability and accuracy of the 3D cellular automata model established in this paper.