Abstract: The soil environment serves as the fundamental basis for plant growth and development. Its diverse physical, chemical, and biological properties profoundly shape plant adaptive evolution and determine agricultural productivity. This review systematically elucidates soil environmental heterogeneity and its “soil imprint” effects on plant origins, and summarizes how soil physical structure, chemical properties, and biological communities regulate plant productivity. We highlight recent advances in the physiological, ecological, and molecular genetic mechanisms underlying plant responses to soil-related stresses. Regarding root system plasticity, plants actively perceive variations in soil mechanical impedance and the localized distribution of nutrients and water. Through hormone-mediated networks involving ethylene and auxin, they remodel root system architecture—such as suppressing primary root elongation while stimulating lateral root proliferation and root hair formation—to optimize resource acquisition. These responses are controlled by key genes, whose natural allelic variations offer promising targets for genetic improvement. In rhizosphere microbe-plant interactions, plants selectively enrich beneficial microorganisms (e.g., nitrogen-fixing bacteria, phosphate-solubilizing bacteria, and mycorrhizal fungi) via root exudates, forming a mutually beneficial rhizosphere community. Studies demonstrate that crop genotype—such as OsNRT1.1B in rice and SWEET2/4/12 in Arabidopsis—strongly influences microbiome assembly, thereby enhancing nutrient acquisition and stress resilience in a coordinated manner. Global climate change alters soil hydrothermal regimes, carbon-nitrogen cycling, and the frequency of extreme events, intensifying stresses such as acidification and salinization. These changes not only reduce crop yields but also lower grain protein and micronutrient concentrations, posing risks to nutritional security. Although crops display phenotypic plasticity and multi-layered molecular responses to these challenges, their synergistic adaptation mechanisms remain insufficiently understood. To address the widespread “soil-blindness” in current breeding systems—that is, the neglect of real-field soil heterogeneity—we propose integrated strategies centered on genetic improvement and smart breeding. First, multi-omics approaches such as genome-wide association studies enable the dissection of the genetic basis of traits related to nutrient-use efficiency, facilitating the identification of key genes governing root development and nitrogen uptake, distribution, and assimilation. These genes can be leveraged through gene editing or molecular design breeding to create nutrient-efficient varieties. Second, coupling the crop “first genome” with the rhizosphere microbiome “second genome”—for example, by regulating carbon allocation and flavonoid-mediated enrichment of Oxalobacteraceae—can synergistically enhance nitrogen and phosphorus use efficiency. Finally, integrating artificial intelligence based predictive models with multi-soil scenario testing will strengthen crop adaptation to soil-specific environments and promote the co-optimization of genotype, environment, and management. Collectively, this framework aims to bridge disciplinary gaps between soil science and breeding, support climate change mitigation, and advance sustainable agricultural development.