Runway roughness is a critical excitation factor during aircraft taxiing, significantly impacting runway service life and the safety of ground operations. To elucidate the mechanism by which roughness excitation influences the dynamic response of the aircraft-runway system, a three-dimensional whole aircraft model considering spatial vibrations and a dual-layer runway structure model incorporating a semi-rigid base were established in this study.  both three-dimensional and two-dimensional runway roughness using measured and simulated data were reconstructed. A novel explicit integration method was introduced to solve and analyze the time-domain responses of the aircraft-runway coupled system, characterized by multiple parameters and high degrees of freedom. The results indicate that under the excitation of measured three-dimensional roughness, the vibration response at the aircraft's forward section is significantly greater than that near its center of gravity. The transverse effect of roughness excitation causes a disparity in the dynamic loads on the left and right main landing gears. Besides vertical vibrations, pitch and roll motions also substantially affect the aircraft's dynamic response. Compared to two-dimensional roughness, the dynamic load coefficient under three-dimensional roughness excitation is 1.20 to 1.52 times that under two-dimensional conditions, and the longitudinal dynamic strain at the bottom layer under three-dimensional roughness excitation is 1.20 to 1.49 times that under two-dimensional conditions. Therefore, the analysis and evaluation of actual runway roughness should shift from two-dimensional to three-dimensional assessments. When runway roughness deteriorates to a poor level according to current standards, the aircraft's vibration response increases exponentially. It is recommended that runway roughness levels be maintained at a medium or higher standard. The degree of runway roughness significantly affects both longitudinal strain and vertical displacement of the pavement, which should be considered in the analysis and design of pavement structures.