The invention belongs to the technical field of the preparation methods of the nanomaterials and specifically discloses a method for preparing water-soluble fluorescent silicon quantum dots by using a hydrothermal process. The method comprises the steps of firstly introducing an amino silane and a reducing agent into a solvent in which nitrogen is introduced and mixing, continuing introducing the nitrogen for protection for a while, next, transferring to a hydrothermal reaction kettle, and heating for reacting for a while, thereby obtaining the fluorescent silicon quantum dots having excellent chemical properties. The method has the advantages of low raw material cost due to the adoption of the amino silane as a silicon source, simple operation steps, direction synthesis in water phase, easy large-scale production, and being green and environment; the obtained quantum dots have high quantum yield and excellent chemical characteristics, and are small in particle size, evenly in distribution, non-toxic, good in biocompatibility and acid resistance; besides, the quantum dots have pH sensitive characteristic in a certain range, and can be widely applied to the biochemical and biomedical sensing fields such as biochemical detection, drug analysis, cell and living imaging and targeting tracing and also can be used as photovoltaic conversion and light-emitting display materials.