Abstract: Alarge amount of data have been accumulated from the agro-ecosystem nutrient cycling research during recent years. It is necessary to develop a data management system for global decision-making and for preserving from loss. This paper outlined a conceptual model design based on Entity-Relation (E-R) model, presented the model constructing process from user query,and demonstrated a database system using a given model. The results showed that the database implemented from the designed model could provide the function of querying in terms of time, location and theme, and management of various types of data, such as field observation, theme map and research report, and fast extracting and analysis data with spatio-temporal characteristic.