The water accumulated in the rutted road sections poses a threat to the safety of vehicles. Water-filled ruts will cause partial or complete loss of the friction between tires and the road surface, leading to driving safety hazards such as hydroplaning and sliding. At present, the maximum water depth of left and right ruts is mostly adopted to analyze the safety of water-filled ruts, ignoring the uneven change of ruts in the driving direction and the cross-section direction, which cannot fully reflect the actual impact of asymmetric or uneven longitudinal ruts on the vehicle. In order to explore the impact of water-filled ruts on driving safety, a three-dimensional (3D) tire-road finite element model is established in this paper to calculate the adhesion coefficient between the tire and the road surface. Moreover, a model of the 3D water-filled rut-adhesion coefficient vehicle is established and simulated by the dynamics software CarSim. In addition, the influence of the water depth difference between the left and right ruts on the driving safety is quantitatively analyzed, and a safety prediction model for the water-filled rut is established. The results of the case study show that (1) the length of dangerous road sections based on vehicle skidding is longer than that based on hydroplaning, and the length of dangerous road sections based on hydroplaning is underestimated by 9.4%–100%; (2) as the vehicle speed drops from 120 km/h to 80 km/h, the length of dangerous road sections obtained based on vehicle sliding analysis is reduced by 93.8%. Therefore, in order to ensure driving safety, the speed limit is controlled within 80 km/h to ensure that the vehicle will not skid. The proposed method provides a good foundation for the vehicles to actively respond to the situation of the water-filled road section.