The ultra-high-speed elevator car–counterweight system will experience substantial aerodynamic effects when operating at high speeds in the annular flow field, particularly at the moment of intersection. These effects will have a considerable impact on the stability of the elevator's operation. This study utilized the unsteady Reynolds-averaged Navier–Stokes approach to investigate the aerodynamic characteristics of the car–counterweight system's entire operation process. The ultra-high-speed elevator three-dimensional transient model is created using dynamic layering mesh technology and then validated through experiments. We investigate the impact of three crucial factors—acceleration, car height, and contact ratio—on the aerodynamic characteristics of the car and the ventilation effect in the hoistway. Specifically, we analyze the instantaneous variations in the aerodynamic force of the car during the intersection process. The results indicate a rapid change in the car's drag and lift at the moment of intersection, with a greater magnitude of change observed in the pressure drag. The acceleration increases gradually, while the drag peak at the intersection time decreases by 1.8%, 3.0%, and 3.6%, respectively. Additionally, the hoistway exhaust volume ratio decreases by 0.9%, 1.5%, and 2.0%. Compared to the drag peak, the lift peak is more responsive to variations in car height. The contact ratio exhibits a sequential increase, but the lift peak demonstrates an uneven upward pattern with increments of 3.07%, 10.35%, and 16.88%. This study greatly enhances the investigation of the aerodynamic characteristics of ultra-high-speed elevators and offers a crucial point of reference for optimizing elevator design in engineering.