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Advances in information technology (IT) and operation technology (OT) accelerate the development of manufacturing systems (MS) consisting of integrated circuits (ICs), modules, and systems, toward Industry 4.0. However, the existing MS does not support comprehensive identity forensics for the whole system, limiting its ability to adapt to equipment authentication difficulties. Furthermore, the development of trust imposed during their crosswise collaborations with suppliers and other manufacturers in the supply chain is poorly maintained. In this paper, a trust chain framework with a comprehensive identification mechanism is implemented for the designed MS system, which is based and created on the private blockchain in conjunction with decentralized database systems to boost the flexibility, traceability, and identification of the IC-module-system. Practical implementations are developed using a functional prototype. First, the decentralized application (DApp) and the smart contracts are proposed for constructing the new trust chain under the proposed comprehensive identification mechanism by using blockchain technology. In addition, the blockchain addresses of IC, module, and system are automatically registered to InterPlanetary File System (IPFS), individually. In addition, their corresponding hierarchical CID (content identifier) values are organized by using Merkle DAG (Directed Acyclic Graph), which is employed via the hierarchical content identifier mechanism (HCIDM) proposed in this paper. Based on insights obtained from this analysis, the trust chain based on HCIDM can be applied to any MS system, for example, this trust chain could be used to prevent the counterfeit modules and ICs employed in the monitoring system of a semiconductor factory environment. The evaluation results show that the proposed scheme could work in practice under the much lower costs, compared to the public blockchain, with a total cost of 0.002094 Ether. Finally, this research is developed an innovation trust chain mechanism that could be provided the system-level security for any MS toward Industrial 4.0 in order to meet the requirements of both manufacturing innovation and product innovation in Sustainable Development Goals (SDGs).