In the era of the digital economy, the task of developing approaches to project management, the subject area of which is at the intersection of IT and real production processes, becomes especially urgent. This clearly demonstrates the challenges of the construction industry, where today the tasks of complex development of territories, the construction of unique facilities and structures are being solved, all based on modern information technologies. In fact, we are talking about a new era in construction — the era of cyber-physical systems. All this predetermines the need to change the methodology of project management in this area. As a methodological basis of project management for the creation of cyber-physical systems in the design, construction and operation of construction sites, an integrated methodological solution is proposed, formed on the basis of the synthesis of methodologies existing in project management. A scheme for the formation of the project management system for the creation of cyber-physical systems is developed on the basis of the project management methodology, which includes elements of project management methodologies such as PMBOK, P2M, PRINCE2, Agile (SCRUM).