This paper chooses a long-span station hall of Beijing South Station as engineering background to evaluate the comfort of “Building-bridge Integration” structures. On the basis of the results of numerical simulation that applies train loads to the structure model at the actual location, dynamic response of the elevated station hall is presented and examined. The result shows that train type and load location significantly influence the structure behavior. Compared with existing standards for structure vibration comfort, the measured vibration intensity is close to or greater than the current specification limits. The actual annoyance rate does not agree with the theoretical value, which indicates that existing comfort evaluation criteria are not suitable to evaluate the comfort of “Building-Bridge integration” structure system.