Transportation engineering focuses on the interaction between people, vehicles, and infrastructures to improve efficiency, safety, and environmental friendliness. Technologies associated with the cooperative vehicle infrastructure system (CVIS), are based on intelligent vehicles, vehicle-to-vehicle communication, and vehicle-to-infrastructure communication. This will eventually transform the transportation system configuration from human-vehicle-road coordination to vehicle-infrastructure cooperation, thereby significantly improving traffic efficiency and safety. In the CVIS environment, conventional human factors have a minimal impact and the intersection of people, vehicles, and roads is enhanced. Traffic systems can be controlled and evaluated effectively, and randomness can be reduced to a large extent. Perception, decision-making, and control are managed by robots instead of people, which could lead to numerous changes and challenges in fundamentals of traditional transportation engineering. In this paper, we will mainly discuss the influence of CVIS on transportation engineering, and the associated scientific issues.