This paper adopts a blockchain fusion neural network algorithm to conduct an in-depth study on the model of agricultural cold chain coordination. We aim to enable HDFS to meet the demand of storing many small files of various types generated by various stages of agricultural cold chain coordination and then propose an improved balanced merging and index caching strategy based on file types and size grouping. The main three modules are the file preprocessing module, file balanced merging module, and index caching module. The experimental results show that this method can significantly improve the overall performance of HDFS when storing and reading large amounts of small files. Simulation experiments using the UCI test dataset show that the improved spectral clustering algorithm not only reduces the error rate but also significantly reduces the time spent on the clustering process, demonstrating the effectiveness and feasibility of the improved spectral clustering algorithm. The improved spectral clustering algorithm of this paper is used to cluster and analyze nearly one thousand cold chain coordination-related data, and the optimal city is successfully selected as the construction point of a large cold storage transit station. This study can effectively improve the efficiency of cold chain coordination resources and their time utilization and maximize the profit creation for cold chain coordination enterprises, selecting data features for prediction, experimenting with different models and parameters to optimize accuracy, and embedding the resulting learning system for prediction and further operations. The two models of coordination market demand forecasting models and methods are analyzed separately. Finally, after analyzing the prediction results of the two different prediction methods, it is found that it conforms to the actual situation of coordination development in Jiangxi Province. It shows that the coordination market prediction model established in this paper is meaningful and the prediction analysis made has some practical value.