While the new generation of smart manufacturing technology is enabling manufacturing upgrades, it is also making manufacturing systems increasingly complex. The integration of information and ontology across the full life cycle of a product involves multi-scientific and multi-disciplinary dimensions. It requires deep integration of industry chain alliance enterprises in the process of domain ontology sharing and digital asset collaboration to achieve efficient "new demand → existing ontology → innovation → new product → new ontology" agile manufacturing paradigm transfer. This paper presents a digital-twin and ontology collaboration framework based on the Industrial Internet Identification and Resolution System (I3R System). Taking flexible manufacturing systems (FMS) as an example, the four core key technologies required in this framework are described in detail: (1) A generic digital-twin modeling approach for the full life cycle of FMS; (2) Ontology for the full life cycle of FMS; (3) Real-time data collection technology for Human-cyber-physical system (HCPS) in smart manufacturing; (4) Distributed collaboration framework based on I3R. In order to illustrate in detail how the proposed methods and techniques can be applied in reality, we show different application scenarios based on the proposed methods and techniques in the various stages of the full FMS life cycle. At the same time, the implementation method of the I3R System-based digital-twin collaborative prototyping platform for industry chain alliance enterprises is discussed, as well as the idea of its derived top-level application.