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The Earth’s surface is a complex system involving mutual interactions of its many components, including mountains, rivers, forests, farmlands, lakes and grasses. The interaction and mutual feedback of chemical elements in Earth's surface layer can drive changes in chemical elemental distribution patterns. In this study, we evaluated the mechanisms and interactions driving the distribution patterns of macroelements, probiotics, halogens and heavy metals in soils in Southwest China, based on a systematic geochemical land-quality survey at a scale of 1:250000. The results showed that the parent material determines the natural state of chemical elements in land resources. Epigenetic geochemical dynamics reshapes the distribution patterns of chemical elements in top soil; biogeochemical processes drive the evolutionary trends of land quality; and human activities, such as mining, disrupt the natural evolution of chemical elemental distribution patterns. The establishment of an epigenetic geochemical dynamics theory allows the construction of a framework for understanding the Earth's surface layer and promoting technological innovations for the comprehensive geochemical investigation of land resources.