With the rapid development of blockchain technology, decentralized cloud storage services are emerging and have been a storage new option in this era. They aim to leverage the unused storage resources across the network to build a more economical and reliable distributed storage network and thus eliminate the trust in the centralized storage providers via matured blockchain consensus mechanisms. However, current solutions either lack the protection of user data privacy or apply conventional encryption methods that cannot support cross-user deduplication over encrypted data. These limitations make them struggle to balance the need for optimized storage space utilization and encrypted data protection, especially in the scenario where the user’s files are geographically distributed in different nodes around the world. In this paper, we propose a secure deduplication system in the context of encrypted decentralized cloud storage. It utilizes smart contract to incorporate the message-locked encryption (MLE) scheme, the most prominent cryptographic primitive in secure data deduplication. With a carefully tailored design, our proposed scheme can be seamlessly deployed to the public blockchain with transparency. Together, our design enables secure data deduplication over decentralized storage, while providing stringent cryptographic data privacy guarantees. In particular, our proposed design has a natural benefit to prevent potential malicious attacks such as file ownership cheating and file ciphertext poisoning. We implement a prototype of our system and deploy it to Ethereum. Comprehensive performance evaluations are conducted with real datasets to demonstrate the effectiveness and efficiency of our design.