The geological disposal of high-level radioactive waste (hereinafter referred to "geological disposal") is a long-term, complex, and systematic scientific project, whose data and information resources in the research and development ((hereinafter referred to "R&D") process provide the significant support for R&D of geological disposal system, and lay a foundation for the long-term stability and safety assessment of repository site. However, the data related to the research and engineering in the sitting of the geological disposal repositories is more complicated (including multi-source, multi-dimension and changeable), the requirements for the data accuracy and comprehensive application has become much higher than before, which lead to the fact that the data model design of geo-information database for the disposal repository are facing more serious challenges. In the essay, data resources of the pre-selected areas of the repository has been comprehensive controlled and systematic analyzed. According to deeply understanding of the application requirements, the research work has made a solution for the key technical problems including reasonable classification system of multi-source data entity, complex logic relations and effective physical storage structures. The new solution has broken through data classification and conventional spatial data the organization model applied in the traditional industry, realized the data organization and integration with the unit of data entities and spatial relationship, which were independent, holonomic and with application significant features in HLW geological disposal. The reasonable, feasible and flexible data conceptual models, logical models and physical models have been established so as to ensure the effective integration and facilitate application development of multi-source data in pre-selected areas for geological disposal.