Mega science projects, with large−scale research facilities as their core carriers, span the full lifecycle from planning and construction to long−term operation and open access; their performance ultimately depends on sustained governance and robust operational mechanisms. This paper takes knowledge discovery mechanisms and organizational governance models as the main analytical lenses and conducts a comparative analysis between China and America. The results show that the United States, relying on a distributed collaboration network connecting national laboratories, universities, and industry, achieves iterative cycles of open access and technology transfer through mature user programs, clearer IP rules, and contract−based management. China, leveraging a new whole−of−nation system and clustered national science centers, demonstrates strengths in strategic alignment and system integration, and promotes technological spillovers and industry coupling through mechanisms such as "spin−offs along the way." Looking ahead to the 15th Five−Year Plan period, mega science projects are expected to exhibit intertwined trends including more complex strategic objectives, ecosystem−based governance, refined operational management, AI and data−driven discovery, and increasingly multi−layered international collaboration. Accordingly, this paper proposes building an integrated "strategy–platform–ecosystem" framework for construction and governance, strengthening operation−phase funding, user governance, and performance evaluation, institutionalizing data governance and AI capabilities, prudently advancing diversified financing and cost−sharing, and enhancing international cooperation and participation in rule−making.