The vent fluids of the Kairei Hydrothermal Field (KHF) on the Central Indian Ridge near the Rodriguez Triple Junction are atypical. They have a very high H2 concentration, relatively high Si concentration, and a significantly low CH4/H2 ratio. Recently, particular attention has been paid to the KHF, because the hydrothermal fluids are suggested to support a hydrogen-based hyperthermophilic subsurface lithoautotrophic microbial ecosystem (HyperSLiME), which is considered to be a likely modern analogue for the early Earth ecosystems prior to photosynthesis. Despite the increasing interest in the fluid chemistry and associated biota, the origin and mechanism to generate the unique chemistry of the hydrothermal fluids is still uncertain. Here, we report the discovery of serpentinized troctolitic rocks from small hills located 15 km east of the KHF, which provide a possible source for the H2-rich hydrothermal fluids. Dives with the manned submersible Shinkai 6500 recovered plagioclase dunite, troctolites, and olivine gabbros, which generally constitute the lower oceanic crust. Microscopic observations revealed that olivine crystals in the samples were partly to completely replaced by serpentine and magnetite, indicating the generation of H2 by serpentinization reactions between olivine and hydrothermal fluids. Theoretical model calculations predict that the low CH4/H2 ratio and high Si content of the hydrothermal fluids can be attributed to serpentinization of the troctolites and subsequent hydrothermal reactions with footwall basalts of the KHF, respectively. Consequently, the unique geological setting of the Kairei hydrothermal system, where deep crustal rocks are emplaced in the shallower part of oceanic crust, is considered to be responsible for the unusual chemistry of the Kairei hydrothermal fluids driving the occurrence of the HyperSLiME.