The exchange of matter and energy between crust and mantle significantly influences the formation and development of oil, gas, and geothermal resources. Understanding how these exchanges impact these resources is crucial in geological science. In many oil-rich basins in China, significant accumulations of H2, CO2, geothermal energy, and other associated resources linked to deep mantle materials or geological processes have been discovered. Therefore, investigating the effects of crust-mantle material and energy exchanges on these resources is of utmost importance. This paper aims to systematically analyze the effects of mantle materials (e.g., H2, CO2, catalytic elements) and energy upwelling into basins. It synthesizes the impacts of various organic-inorganic interactions on hydrocarbon generation, evolution of organic source rocks, reservoir development, and the formation and accumulation of oil and gas. Finally, it proposes a mechanism detailing how interactions between mantle matter and energy influence specific resources. Simultaneously, this study employs numerical simulations to uncover the specific impact of magma intrusions on the geothermal field of surrounding rock formations. It demonstrates that magma chambers, continuously supplied with mantle energy, create regional thermal anomalies and facilitate the development of high-temperature geothermal resources. This underscores that mantle materials and energy not only significantly influence the generation of oil and gas but also govern the formation of geothermal resources and the evolution of thermal reservoirs. This research provides a theoretical foundation for understanding the subsequent formation of oil and gas resources under the influence of deep geological processes. Moreover, it furnishes a scientific basis for evaluating and exploring the symbiotic relationship between oil and gas resources and geothermal reservoirs.