From the perspective of the recent advance of spatial database modeling technology, this paper deeply analyses data classification and their characters of the Yangtze River Ecoa2environment Information Database(YREID), introduces basic concepts of GeoDatabase model, and attempts to manage and organize these data using GeoDatabase model. Then it provides data organization of feature dataset, raster dataset and TIN dataset in YREID, and discusses the links between spatial database and attribute database. Finally, model evaluation and its future advance are also presented.