With the rapid development and widespread application of emerging technologies such as blockchain, the Decentralized Science (DeSci) movement has emerged, aiming to improve the traditional centralized scientific system and build an open and inclusive autonomous scientific ecosystem. To address challenges in the centralized scientific system, including issues in information flow, resource allocation, and evaluation mechanisms, the operational mechanisms of blockchain-based DeSci system were reviewed. Firstly, the concept of DeSci and its current applications were introduced. Secondly, through a literature review of DeSci, the operational mechanisms of scientific systems were classified into four aspects — asset management, token economics, organizational governance, and trust construction — from both economic and social perspectives. The current state of the scientific system and the advantages of blockchain technology in addressing existing limitations were summarized according to these categories. Next, the operational mechanisms of decentralized scientific systems based on blockchain and related technologies were analyzed in detail. Finally, the future decentralized scientific ecosystem was explored from the perspective of the entire scientific research process, with challenges and future opportunities faced by decentralized scientific system practices discussed. The review suggests that blockchain-based DeSci systems have the potential to enhance the existing scientific framework, and their operational mechanisms can provide both theoretical foundation and practical directions for developing an autonomous scientific ecosystem.