Low-temperature hydrothermal system is dominated by Fe-Si oxyhydroxide deposits. However, the formation process and mechanism on modern hydrothermal Fe-Si oxyhydroxides at ultra-slow spreading centers remain poorly understood. The investigation presented in this paper focuses on six Fe-Si deposits collected from different sites at the Southwest Indian Ridge (SWIR). The mineralogical and geochemical evidence showed significant characteristics of a low-temperature hydrothermal origin. The Mössbauer spectra and iron speciation data further provided an insight into iron-bearing phases in all deposits. Two different types of biomineralized forms were discovered in these deposits by Scanning Electron Microscopy analysis. Energy-dispersive X-ray spectrometry and nano secondary ion mass spectrometry revealed that distinct biogenic structures were mainly composed of Fe, Si, and O, together with some trace elements. The Sr and Nd isotope compositions of Fe-Si deposits at the SWIR were closely related to interaction between hydrothermal fluids and seawater. The remarkably homogeneous Pb isotope compositions can be attributed to hydrothermal circulation. Based on these findings, we suggest that microbial activity plays a significant role in the formation of Fe-Si oxyhydroxides at the at ultra-slow spreading SWIR. Biogenic Fe-Si oxyhydroxides potentially provide insights into the origin and evolution of life in the geologic record.