In Industry 4.0, a network of enterprises and factories is constructed collaboratively and dynamically according to the cyber physical system (CPS) paradigm. It is necessary to build smart supply chains according to this concept. A network of component enterprises in a supply chain would be modeled as a virtual supply chain in the cyber world. From the viewpoint of Industry 4.0, virtualizing a supply chain is the foundation for constructing a CPS for a supply chain. The virtualization of a supply chain makes it easier for companies to study their integrating and expanding opportunities. By using this CPS, comprehensive and autonomous optimization of the supply chain can be achieved. This virtual supply chain can be used to simulate the planning phase with negotiation, as well as the production phase. In this paper, instead of specific mathematical modeling for each supply chain, a general configuration method of a virtual supply chain is proposed. The configuration method of a supply chain model is proposed as a virtual supply chain using enterprise e-catalogues. A virtual supply chain is constructed as a multi-agent system, which is connections of software agents that are automatically created from each selected enterprise model in the e-catalogues. Three types of component enterprise models are provided: manufacturer model, part/material supplier model, and retailer model. Modeling templates for these three types of enterprises are prepared, and each template is a nominal model in terms of enterprise’s behavior. Specific component-enterprise models are prepared by filling the appropriate template. Each component enterprise agent is implemented using the enterprise model selected from the catalogues. Manufacturer, retailer, and supplier e-catalogues, as well as an automatic construction system of a virtual supply chain, are implemented. Methods for developing templates for the manufacturer, retailer and supplier were provided, and the construction system for specific enterprise models (as e-catalogues) is implemented as a trial.