The application of a semi-flexible pavement (SFP) is an effective solution to solve the rutting problems of the autonomous rail rapid transit (ART) system. The service environment of an ART pavement is significantly different from that of the conventional pavement due to the large axle load and high tire pressure of ART vehicles. A test section was constructed in the Zhuzhou ART system and a tire–pavement coupling FE model was built to explore the distribution features of the dynamic responses as well as to optimize the material and structural design. The tire–pavement coupling model was firstly verified by the field test data and then, utilizing the validated model, the parameter study was performed to analyze the influence of the vehicle operating state and pavement conditions. The simulation results show that the transverse tensile strain at the bottom of the SFP layer is dominant for the fatigue cracking of the pavement. Properly reducing the tire pressure can effectively improve the tensile environment at the bottom of the SFP layer. The action of the braking force may cause significant longitudinal tensile strains at the surface of the SFP layer and lead to transverse cracking of the semi-flexible ART pavement. The interlayer bonding between the SFP layer and the asphalt layer has significant influence on the amplitude and distribution of tensile stress at the bottom of the SFP layer. Moreover, to optimize the tensile environment of the semi-flexible ART pavement, the thickness of the SFP layer and the asphalt concrete layer cannot differ too much under the premise of meeting the requirements of rutting resistance performance.