With rail transit construction developing by leaps and bounds in China, the traditional project management model has shown discomfort. Informatization management, the modern concept of project management, provides a new management model for rail transit construction management and becomes an effective way to change the shortcomings of traditional project management. This paper bases on the analysis of the characteristics and requirements of the rail transit construction management, presents the informatization management system based on integrated management thoughts and analyses its overall frame and operation mechanism virtual reality, decision support and dynamic control. Then, it proposes to strengthen the constructions in three aspects including the organizational and institutional, runtime environment of informatization platform and informatization technology to ensure the informatization management system of rail transit construction running safely and smoothly.