The relevance of developing knowledge-based systems used to support innovative processes for creating products and services is related to the objective need to reduce the life cycle of products under the influence of modern digital technologies in developing network enterprises. Well-known research results in the field of model-oriented design of products, processes, systems and enterprises do not fully provide semantic interoperability in the interaction of stakeholders in the innovation process. The aim of this work is to build a knowledge-based system architecture that implements semantic interoperability of network enterprise participants at various stages of the product lifecycle. The work is based on the use of a model-oriented approach to building a digital thread at all stages of the product lifecycle, an ontological approach to semantic modeling of a distributed knowledge base and a multi-agent approach to organizing interaction between interested participants in the innovation process. The paper proposes a functional architecture of a knowledge-based system that includes modules for planning the innovation process, forming product value characteristics and functional requirements, construction and value chain design. A multi-level system of ontologies of the innovation process is also developed and its application in the work of functional modules that provide access to associated knowledge bases is described. The development of knowledge-based systems based on the results obtained will allow us to find the best design solutions for the configuration of products and corresponding value chains due to the possible iteration of the innovation process and increasing the semantic interoperability of network enterprise stakeholders.