The conceptual framework of agricultural production factors has long been anchored in a static-triad paradigm encompassing land, labor, and capital. This traditional model faces persistent challenges in surmounting the bottlenecks that impede the qualitative advancement of agricultural productive forces. A critical imperative thus emerges: to fundamentally reconfigure the operational logic and redefine the boundary dimensions of the agricultural system through the innovative allocation of production factors. This transformation is essential to establish a foundational underpinning for cultivating agricultural new quality productive forces. Accordingly, this study constructs a theoretical framework positioning the innovative allocation of production factors as a fundamental driver of agricultural newquality productive forces, conducts a diagnostic assessment of the core bottlenecks hindering the innovative allocation of agricultural production factors, and further proposes corresponding policy suggestions. Our investigation reveals: innovation in traditional factors is constrained by: persistent structural contradictions coupled with an aging workforce; dual bottlenecks comprising inefficient land transfer mechanisms and land fragmentation; and a diminishing trend in capital input. Innovation in emerging factors confronts practical challenges such as: the dual constraints of ″digital incapacity″ and lagging institutional supply; and ethical and biosafety risks inherent in the application of emerging technologies (e.g., biotechnology). The transition between traditional (″old″) and emerging (″new″) factors is hampered by structural contradictions: insufficient investment in agricultural science and technology; fragmented governance structures and platform deficiencies that impede structural coupling; and divergent factor attributes that complicate systemic adaptability,consequently escalating the difficulty of institutional regulation. To address these challenges, it is imperative to adhere to Xi Jinping Thought on Socialism with Chinese Characteristics for the New Era, uphold the principles of preserving the essence while fostering innovation and prioritizing people-centered development. Guided by a tripartite strategic approach—entailing institutional supply, technology-driven development, and robust data governance—we advocate a phased implementation pathway. This involves short-term breakthroughs, mid-term deepening, and long-term restructuring. Concretely, this requires optimizing the allocation of traditional factors, systematically deploying the innovative application of emerging factors, and synergistically resolving the structural contradictions inherent in the old-new factor transition.