As one of the unconventional intersection designs, the median U-turn (MUT) intersection design has been confirmed to have the potential to improve intersection efficiency and produce lower vehicle delays, and it has been widely applied to many urban networks. Most existing studies have successfully evaluated the operational performance of MUT intersections by analyzing the overall traffic flow, particularly for intersection delay and capacity. However, the impact of the critical parameters and behavior of individual vehicles in MUT intersection operations has not been adequately studied. These limitations cannot provide a complete and objective evaluation of MUT intersections. Therefore, a comprehensive cellular automata model is proposed to simulate vehicle dynamic variations, considering road channelization information and vehicle random movements. This model will be compared to the VISSIM model to validate rationality by using field data, and it shows a good agreement between the simulation results of both models. In addition, sensitive experiments reveal that properly adjusting the elements, including the separation distance, the proportion of left-turn vehicles, and green phase percentage, can improve the operation of MUT intersections to varying degrees. By appropriately improving intersection features and conducting reasonable evaluations, the overall performance and sustainability of the MUT intersections in Xi’an city can be enhanced. Finally, this paper offers a valuable guideline for the evaluation and modeling strategies of MUT intersections.