Green transformation is essential for achieving high-quality development and modernization in agriculture. New quality productivity play a pivotal role in promoting agricultural green ransformation. In comparison, agriculture possesses strong natural attributes and overlapping social attributes, and various links in the agricultural industry chain face more complex objective orrelations and mutual influences. Therefore, it is imperative to pursue a robust transformation of the entire agricultural industry chain, considering both the natural and social systems. This approach aligns erfectly with the essence of the new quality productivity. Guided by Marx’s theory of productivity and aiming to improve total factor productivity, this paper explains the economic logic of new quality productivity promoting the green transformation of the agricultural industry chain from two aspects: the allocation balance of production factors and the dynamic balance of the industrial chain. Furthermore, the aper summarizes the realistic conditions for new quality productivity to drive the green transformation of the agricultural industry chain, considering aspects such as industrial integration, scientific and echnological support, public demand, and policy backing. Then, the paper highlights the challenges currently faced by the agricultural green transformation, including inadequate connections in the ndustrial chain, insufficient support for green technology, a shortage of highly skilled agricultural professionals, limited ecological value-added effects, and a dearth of diverse governance entities. To address these challenges, the paper emphasizes the need to optimize the green development system of the agricultural industry chain, build the green industrial science and technology chain, cultivate a highly skilled talent pool, expand the agricultural ecological space, and foster multi-agent coordination and collaborative governance.