The development of transportation engineering is performed with a focus on the coupling between human, vehicles, and roads to improve the level of efficiency, safety, and environmental friendliness. Technologies associated with the cooperative vehicle infrastructure system (CVIS), which is based on the concepts of intelligent vehicles and V2V and V2I communication, will cause the transportation system configuration to gradually change from human-vehicle-road coordination to vehicle-infrastructure cooperation, thereby greatly improving traffic efficiency and safety. Under the CVIS environment, conventional human factors affecting traffic have less influence, and the coupling of human-vehicle-road is enhanced; thus, the systems can be controlled and evaluated effectively, and the randomness in traffic systems can be reduced. The processes of perception, decision-making, and control are performed by robots instead of humans, and this could lead to numerous changes and challenges to the theory of transportation. This paper discusses the influence of CVIS on transportation engineering, and the associated scientific issues.