As a major source of greenhouse gas emissions, agriculture’s green and low-carbon transformation is crucial for achieving coordinated development of ecological security and food security. This paper analyzes the systemic challenges facing China’s agricultural green and low-carbon transformation from three dimensions—technology, economics, and structure—including inadequate technology adaptation and diffusion barriers, input shortages and imbalanced return cycles, regional development imbalances, and extensive industrial structures. Building on this analysis, the paper proposes a three-pronged transformation pathway—“technology convergence to empower production optimization, factor restructuring to strengthen economic support, and structural adjustment to drive coordinated development”—by integrating perspectives on digital economy empowerment, technological innovation-driven approaches, and institutional coordination safeguards. This framework aims to provide theoretical reference and practical insights for China’s sustainable agricultural development and the achievement of its dual carbon goals.