Digital transformation of heterogeneous enterprises and infrastructures is costly and error-prone without a unified representation of data and processes across interacting subsystems. This paper proposes a systemic approach grounded in the theory of polystructural systems and formulates a System-of-Systems (SoS) topology of information space as a central organizing mechanism for integrating heterogeneous information arrays. To ensure universality and reduce coupling to domain-specific schemas, we introduce a set of invariant information structures and rules for organizing collinear and named connections, enabling consistent representation of goals, objects, processes, and indicators. The key novelty is an object-centric query mechanism that replaces static database key/index logic with first-class information objects: “Relationship” and “Relationship between two Relationships”. These objects act as dynamic data sources for constructing information requests and support rapid recomposition of queries when new tasks emerge. This property is particularly valuable under unforeseen conditions (e.g., natural disasters or technogenic incidents) where operational processes and data dependencies change abruptly. The paper details the construction workflow for the proposed topology, including goal-tree integration via a polymetric system, and illustrates the approach through representative diagrams that can be reused as design patterns for digital transformation tools in heterogeneous SoS environments.