With the rapid construction of high-speed railways (HSR), the supply structure of the transportation modes in China has changed greatly. In order to seek the sustainable development of HSR and air transport from the perspective of passenger mode choice behavior, this paper applied a binary logit model to explore the mode choice patterns in the Beijing–Shanghai corridor, which has the most successfully operated HSR line in China. By using the data collected in airports and HSR stations in the two cities, passenger flow composition and passenger mode choice behavior was analyzed. It was found that passengers’ preference for air transport decreases with the accompanying number of passengers and access time, and increases with income; female passengers and younger passengers have a higher probability of choosing air transport, ceteris paribus; and leisure passengers are more price-sensitive, they tend to travel by air transport when the air transport prices are lower. The study results reveal the travel characteristics of passengers between Beijing–Shanghai and provide information for policy design and infrastructure management.