The invention provides a multi-data center based natural resource geospatial data organization method and system. The method comprises a data type identification step, a feature class model establishment step, a relation class data model establishment step and an auxiliary information acquisition step. Firstly, the type of natural resource geospatial data is identified and data centers, a database, a data set and an auxiliary information set are established; secondly, according to the identified data type, establishing a feature class data integration organization model and establishing a relation class data model; and finally, according to the identified data type and a relation class data calculation result, acquiring auxiliary information and storing the auxiliary information in the auxiliary information set. According to the organization method provided by the invention, unification of different data types in a conception layer based on a plurality of data centers and integration organization management of different data types are realized; orderly data management and data tracking and backtracking are realized; and the application convenience and flexibility of the natural resource geospatial data are satisfied.