Abstract: Collaborative innovation is an important part of the high-quality development of clustered agricultural e-commerce firms. It is of great significance to realize the effective connection between small-scale production and large-scale consumption and the development of agricultural modernization. Based on a micro survey data of 358 clustered agricultural e-commerce firms in Hubei, Jiangxi and Zhejiang provinces, this paper adopts the multi-level regression analysis and the bootstrap analysis methods to analyze the relationship among geographical concentration, dual knowledge network embedding, and collaborative innovation performance of clustered agricultural e-commerce firms and to explore the moderating effect of asset specificity and environmental uncertainty. Results show that the geographical concentration and collaborative innovation performance of clustered agricultural e-commerce firms are at a high level, while dual knowledge network embedding, asset specificity, and environmental uncertainty are at a medium level. Geographical concentration, dual knowledge network embedding, and asset specificity are positively correlated with collaborative innovation performance, while environmental uncertainty is negatively correlated with it. Geographical concentration of clustered agricultural e-commerce firms positively affects collaborative innovation performance. Dual knowledge network embedding plays a partial mediating role between geographical concentration and collaborative innovation performance. Asset specificity positively moderates the positive relationship between dual knowledge network embedding and collaborative innovation performance, while environmental uncertainty plays a negative moderating role. Meanwhile, asset specificity and environmental uncertainty jointly moderate the positive relationship between dual knowledge network embedding and collaborative innovation performance. Therefore, clustered agricultural e-commerce firms should strengthen cooperative innovation with internal and external firms of cluster, pay attention to the input and renewal of digital technology equipment, build competitive advantages based on knowledge resources, grasp development opportunities in an uncertain environment, and realize high-quality collaborative innovation development.