The construction of mega infrastructure projects has the characteristics of repeatability, long duration, and high complexity. Therefore, it is particularly important to implement dynamic decision-making in projects. This study takes data-driven decision-making mechanisms as the entry point and constructs a dynamic decision-making system for mega infrastructure projects consisting of an information collection subsystem, an information processing and transformation subsystem, a human–computer collaborative decision-making subsystem and an evaluation and feedback subsystem. On this basis, we established a system dynamics model of dynamic decision-making for mega infrastructure projects. Vensim PLE 9.3.5 software was used to simulate and analyze the operation law of dynamic decision-making for mega infrastructure projects from a data-driven perspective, and the sensitivity of the application rate of information management technology, the application rate of data analysis methods, the participation rate of experts in decision-making, the historical case information on this project, and the information on similar projects on the effectiveness of program implementation were simulated and analyzed. The results of the study showed that all five key influencing factors have a positive impact on the effectiveness of program implementation. In addition, the application rate of information management technology and the application rate of information analysis methods have a higher sensitivity to the effectiveness of program implementation, the participation rate of experts in decision-making and historical case information on this project have average sensitivity to the effectiveness of program implementation, and information on similar projects has lower sensitivity to the effectiveness of program implementation. This study provides some ideas and suggestions to promote the effective use of information technology and digital technology by each participant in the construction of mega infrastructure projects while improving their dynamic decision-making efficiency, scientificity, and accuracy.