Abstract: This paper is the result of basic geological engineering. Objective As a key component of the Earth's surface system, the ground substrate serves as the core carrier for material cycling and energy flow within ecosystems. Its spatial heterogeneity pattern profoundly influences ecological processes, biodiversity, and system functions. However, existing research exhibits significant theoretical gaps, particularly the lack of a systematic framework integrating geological and ecological processes. This limitation hinders the practical implementation of geological survey projects. To address this, this study employs an Earth System Science perspective to define the connotation and characteristics of ground substrate spatial heterogeneity, constructs a theoretical framework, and systematically elucidates its formation mechanisms, multi-scale effects, and ecological service functions. This aims to fill the theoretical void and provide methodological guidance for the field. Methods This study adopts a systematic approach centered on interdisciplinary theoretical integration, following a “literature review–concept definition–theoretical integration–paradigm construction” pathway. It reviews core advances and theoretical gaps in research on ground substrate and spatial heterogeneity, and proposes an “ecosystem–geological process” feedback theory and a “surface process–biodiversity” correlation theory, establishing a multi-level, multi-process coupled systematic theoretical framework. Results The study defines the conceptual system of spatial heterogeneity of ground substrate, revealing its multi-scale dependency, structure–function complexity, dynamic evolution, patch mosaic characteristics, and environmental gradient responsiveness. A multidisciplinary integrated framework was constructed, forming a theoretical paradigm centered on “driving mechanisms–spatial patterns–ecological processes–service functions.” A research content and methodology system was established, covering substrate attribute distribution, causes of heterogeneity, relationship with ecological processes, scale effects, and service functions. Methodologically, a technical chain of “data acquisition–spatial analysis–mechanism simulation–effect assessment” was proposed. The mechanism of interaction between spatial heterogeneity and ecosystem structure, processes, and services was elucidated. It was demonstrated that spatial heterogeneity regulates the distribution of water and nutrients, influences species composition, community dynamics, and key ecological processes, serving as a foundation for maintaining biodiversity and enhancing ecosystem stability. Conclusions From the perspective of Earth system science, this study constructs a theoretical paradigm for spatial heterogeneity of ground substrate, highlighting its key role in connecting subsurface geological processes with surface ecological functions. The framework integrates multidisciplinary theories and methods, systematically explaining the formation mechanisms, scale-related patterns, and ecological effects of heterogeneity. It holds significant theoretical and practical value for maintaining biodiversity and enhancing ecosystem services. The research advances the field from phenomenological description to mechanistic analysis and theoretical construction, providing a scientific basis for interdisciplinary integration and regional sustainable development. Future work can conduct empirical studies across multiple regions and scales based on this paradigm, promoting integrated “theory–method–practice” development.