From the 1960s to the present, GIS has undergone a development journey of over 60 years, during which its connotations have evolved from geographic information system (GISystem) to geographic information science (GIScience), and further to geographic information service (GIService). During this period, GIS research has primarily been based on the two-dimensional abstract expression logic of cartography (Map-based GIS), achieving abstract analysis and representation of the real world. However, with the continuous emergence of new technologies and new demands such as 3D real scene, digital twins, and city information modeling (CIM), the original two-dimensional logic of GIS is facing challenges in the collection, processing, and fusion of multi-source heterogeneous spatiotemporal big data, the representation of complex spatiotemporal dynamic processes, and the mining of potential spatiotemporal patterns. How to adjust the scientific positioning of GIS to adapt to the multi-type, multi-level, and multi-role needs of spatial object expression and analysis in the digital society has become an important issue that GIS development urgently needs to consider. From a methodological perspective, we deeply analyzes the bottlenecks of Map-based GIS in spatial representation, spatial analysis, and comprehensive application. Furthermore, based on the development needs of GIS in the new era, we propose a scientific concept transformation model from Map-based GIS to Space-oriented GIS, integrating the logical thinking of Map-based GIS from the perspectives of theoretical foundations, management models, visualization forms, and functional positioning, and innovative applications under the transformation of GIS scientific concepts. This research aims to provide reference ideas for the development of GIS in the new era.