In order to solve the safety problems encountered when aircraft land and taxi on runway surfaces with accumulated water, three-dimensional random uneven half-runway surfaces with different flatness grades were established. The distribution of accumulated water in the landing strip under the influence of runway unevenness was used to investigate the accumulated water distribution characteristic matrix. Moreover, a theoretical model for aircraft landing and taxiing on runways with accumulated water was established, and dynamic simulations were carried out using the Simulink tool to analyze the impact of runways on aircraft landing performance under different accumulated water distribution conditions. The results show that compared with "good" (international roughness index, IRI = 1), the landing distance of the runway with "poor" (IRI = 5) increases by about 29 m, and the landing distance of the runway with "poor" (IRI = 1) increases by 3.7% compared with the ideal smooth road. Moreover, the decrease of road smoothness would aggravate the risk of tire water skiing. If the ground speed of the aircraft is increased from 62 m/s to 82 m/s, the landing distance will directly increase by about 520 m, an increase of about 87%. When the rainfall intensity of 1 mm/min increases from 1 mm/min to 3 mm/min, the landing distance increases by 6.5 m and 7.4 m for each increase in rainfall intensity of 1 mm/min. It is concluded that at the uneven position of the pavement, the greater the grounding speed, the greater the speed when reaching the same position, and the greater the reduction of the adhesion coefficient of the position, up to 11.3%. With the increase of rainfall intensity, the adhesion coefficient decreases gradually. When the rainfall intensity reaches 3 mm/min, the adhesion coefficient decreases by about 20% compared with the dry pavement.