Abstract: Protected agriculture plays a crucial role in ensuring food security, optimizing the agricultural production structure, and promoting the development of modern agriculture. However, its development in China faces challenges such as insufficient policy coordination and uneven resource allocation. This study aims to explore the structural characteristics, developmental trajectory, and internal logic of China’s protected agriculture policy, providing theoretical support and decision-making references for optimizing the governance system and enhancing policy effectiveness. Based on national-level policy documents issued from 1999 to 2024, this paper employs policy bibliometric analysis and content analysis to construct an analytical framework centered on “policy structure–policy instruments–policy evolution”, systematically revealing the evolutionary patterns of China’s protected agriculture policies. The findings show that: 1) in terms of policy structure, the number of policies issued at the central level has shown phased and fluctuating growth, with increasingly diversified policy actors and a system characterized by implementation orientation; 2) in terms of policy instruments, there exists a structural imbalance described as “strong environmental orientation, weak supply orientation, and insufficient demand orientation,” where environmental instruments are most frequently applied, followed by supply-side instruments, while demand-side tools are relatively underused; 3) in terms of policy evolution, the development of protected agriculture policies follows a progressive trajectory from lower-order to higher-order stages, with distinct priorities at each stage. Accordingly, China’s future protected agriculture policymaking should focus on improving the stability of policy issuance and strengthening medium- and long-term development mechanisms; enhancing coordination among policy actors and increasing top-level institutional supply; and balancing the configuration of policy instruments to improve overall policy performance.