Spatial intelligence requires agents to form and utilize internal representations of the physical world for perception, reasoning, and generation. While recent advances in foundation models, embodied systems, and three-dimensional representation learning have substantially expanded spatial capabilities, existing research remains fragmented across heterogeneous tasks and model paradigms. This survey revisits spatial intelligence from a cognitive map perspective and positions cognitive maps as its representational blueprint. In this view, diverse lines of research can be understood through a shared question: how an internal spatial representation is constructed, maintained, reasoned over, and realized. To make this perspective operational, we define cognitive maps as internal spatial representations characterized by abstraction, globality, and persistency. Based on this definition, we organize the literature into three cognitive-map-centric processes that correspond to the core dimensions of spatial intelligence: perception for cognitive map construction, reasoning for internal inference with the map, and generation for external realization of the map. By adopting a mechanism-centric viewpoint, this survey connects previously isolated research directions into a coherent framework and identifies emerging challenges toward unified spatial intelligence systems. The related resources of this study are accessible at https://github.com/Klingsor-tyx/Awesome-Spatial-Cognitive-Map.