The invention provides a multi-stage vibration isolation system for a precise instrument, first deep groove vibration isolation trenches are annularly arranged in a foundation, and the first deep groove vibration isolation trenches are used for dividing the foundation into an outer foundation and an inner foundation; a precise instrument is arranged on the inner foundation, and the first deep groove vibration isolation trenches are filled with the first vibration isolation medium, so that vibration reduction is performed in multiple aspects, vibration excited by a moving part and ground low-frequency random vibration can be decoupled, and vibration on the main substrate is reduced from a vibration source by blocking a transmission path of disturbance force of the moving part. Different high-damping vibration isolation materials are selected as first vibration isolation media according to broadband vibration and narrow-band vibration, the first deep groove vibration isolation grooves are filled in a series connection mode so as to meet the high-precision requirement for silicon wafer positioning, in this way, moving parts and the main substrate are separated through the vibration isolators, vibration sources can be reduced, vibration is greatly reduced, and the motion positioning precision of a silicon wafer in a photoetching machine is improved.