Urban agglomerations serve as essential platforms for regional innovation, while agricultural technology innovation and diffusion play pivotal roles in enhancing agricultural eco-efficiency (AEE). Based on panel data from the Urban Agglomeration in the Middle Reaches of the Yangtze River (UAMRYR) (2001–2023), this study employs a super-efficiency slacks-based measure model incorporating undesirable outputs to evaluate agricultural eco-efficiency. A modified gravity model is utilized to construct agricultural technology innovation networks (ATINs) in urban agglomerations, and a spatial Durbin model is applied to examine the spillover effects of network structure on eco-efficiency. The results indicate that: (1) Higher-degree centrality within the innovation network significantly improves local agricultural eco-efficiency and produces positive spillover effects on neighboring cities; (2) both direct and spillover effects are significant in central cities, whereas sub-central cities exhibit only a significant direct effect, and peripheral cities display an insignificant direct effect but a significant spillover effect; and (3) enhanced urban informatization, agricultural financial development, and industrial scale substantially strengthen the spatial spillover effects of the innovation network, thereby further advancing agricultural eco-efficiency within the agglomeration. These findings offer theoretical and empirical support for optimizing agricultural technology pathways and enhancing eco-efficiency in urban agglomerations.