With the rapid development of China's economy, the agricultural industry chain has a new mode of operation. The rise of big data technology can collect the relevant information of the agricultural industry chain in all aspects more rapidly, accurately and comprehensively, so that the agricultural production, logistics and information flow can be unified, so as to realize the optimization of the resource structure of the industrial chain, and the operation efficiency is higher. In this paper, the analysis method combined with big data was used to construct the industrial chain of ecological agriculture. The ecological agriculture industry in Wuwei was regarded as the specific research object, and a large amount of empirical data was collected by means of consulting literatures and field surveys. The input analysis and output analysis of the agricultural production in Wuwei were carried out and the original industrial chain model was evaluated, and the deficiency of the influence factors was improved. The agricultural industry chain was the developmental situation of a dynamic organization, which had important methodological significances. This paper attempted to put forward some suggestions for the rational development of the agricultural industry chain.