Tight schedules, multifunctional scopes, and colossal sizes usually characterize transportation megaprojects as challenging tasks for completion. In order to address these situations, a schedule risk management method was developed in this paper based on the structural equation model. In the proposed method, risk identification, evaluation and response were arranged as a sequence, and the expert elicitation technique was adopted in order to quantify the schedule risk status. To demonstrate the applicability of the proposed model, a megaproject case in China, the Shanghai Hongqiao Integrated Transport Hub (SHITH), was chosen. Information within the expanded risk register was collected including the probability and consequence of risk events, the complexity of risk responsible owners, the reaction time, and the time lasting for risk countermeasures. Final risk control results showed that the method could not only address the schedule risks correlations effectively, but also maintained the simplicity for construction management practices.