The paper considers the methodology of synchronizing visual models of the system project through knowledge XML templates. The object of study is the means of formal description, storage, and transfer of design information about complex systems in the context of digital industry transformation. A new concept of system analysis of complex systems and the generalized design environment which implements it are analyzed. The study suggests a concept of cognitive metalanguage VI-XML implementing metaphors of cognitive visualization, taking into account the synchronization of different abstraction levels. This allows the encapsulation of visual metaphors of different abstraction levels into a single closed multi-level system model. Methods of establishing correspondence between the elements of heterogeneous diagrams of visual models are proposed, and the mechanism of translating component representation of the diagram to VI-XML and vice versa based on knowledge paradigms is substantiated. The proposed method is based on the integrated adaptive visual design environment, which analyzes components of visual-conceptual, structural-functional, and object models of various notations in a single decision tree. The method provides an efficient and adequate representation of the subject area knowledge in multi-level visual models and implementation of management tools in terms of their evolutionary development and adaptation to the demands of the system project.