High performance processing of agricultural data in the grid environment is a complex and difficult problem, mainly due to agricultural data geographic distribution, heterogeneity and variety. A multi-layered software architecture for agricultural data grid system was designed. Agricultural meta-data model based spatio-temporal ontology, spatial clustering and mapping for agricultural data, information cooperation, role-based access control were researched. The application environment of agricultural data grid node was constructed. The inspection experiment indicates that the agricultural data grid system provides high performance computation and communication capability.