New-quality productive forces serve as the core engine for promoting the high-quality development of agriculture and improving the total factor productivity of agricultural product industrial chains. Based on the theory of new-quality productive forces, this paper analyzes the practical bottlenecks restricting the development of current agricultural product industrial chains, and reveals that the three-dimensional synergistic mechanism consisting of revolutionary technological breakthroughs, innovative factor allocation, and in-depth industrial transformation and upgrading drives the improvement of total factor productivity in agricultural product industrial chains. At this stage, China’s agricultural product industrial chains still face multiple dilemmas, including insufficient adaptation between technology supply and demand, blocked flow of high-end factors, loose interest linkage among market entities, and imperfect policy and institutional support, which restrict the full release of the empowering effect of new-quality productive forces. Accordingly, this paper proposes optimization paths from four aspects: strengthening key core technology research and achievement transformation, smoothing the flow channels of high-end factors, reshaping the structural resilience of industrial chains, and deepening institutional and mechanism reforms. This study aims to improve the theoretical system of agricultural industrial chains empowered by new-quality productive forces, and provide practical references for advancing the modernization of agricultural product industrial chains, enhancing agricultural total factor productivity, and facilitating the high-quality development of agriculture.