Deep-sea hydrothermal vents are among the habitats that host the most diverse microbial communities on the Earth. It is promised that hydrothermal vent microbial communities play a major role in the circulation of energy and materials in the global oceanic and suboceanic environments, and even provide important insights into the origin and early evolution of life on the Earth and extraterrestrial life on other planets and moons. Deep-sea hydrothermal vent ecosystems are strongly dependent on the primary production of symbiotic and free-living chemolithoautotrophic microorganisms that can obtain energy from inorganic substances such as H2S, CO2, H2, and CH4 derived from hydrothermal vent fluids. The diversity and abundance of these energy and carbon sources at hydrothermal vent fluids are, in turn, controlled by subseafloor physical and chemical processes such as fluid-rock interactions and phase-separation and-partition of fluids. Therefore, linkage between rock (magma) , hydrothermal fluid, and ecosystem is a key to understanding how deep-sea hydrothermal ecosystems are generated and sustained. In this article, we approach this whole "Rock-Fluid-Ecosystem linkage" with the two separate sub-linkages of "Rock-Fluid linkage" and "Fluid-Ecosystem linkage" , which have not been addressed by the individual research fields of the Geochemistry of Hydrothermal Systems and Hydrothermal Vent Microbiology, respectively. Here, we overview the progress of understanding the "Rock-Fluid" and "Fluid-Ecosystem" linkages, both of which will establish the basis for an integrated "Rock-Fluid-Ecosystem linkage". In seafloor hydrothermal systems, three major physical and chemical processes affect hydrothermal fluid chemistry: (1) chemical interactions between rock and hydrothermal fluid, (2) volatile inputs from magmas, and (3) phase-separation and-partition of hydrothermal fluids. The chemistry of hydrothermal fluids is primarily controlled by subseafloor fluid-rock interactions, and chemical behavior during fluid-rock interactions is constrained by phase equilibria among primary and secondary minerals in rocks. Therefore, the chemical compositions of rocks and pressure-temperature conditions of fluid-rock reactions play dominant roles in controlling fluid chemistry. Volatile inputs from magma to hydrothermal fluid are conspicuous in arc-back arc hydrothermal systems, due to the remarkable enrichment of