The invention discloses a scanning electron microscope direct-writing photoetching system based on a flexible nano servo motion system. The scanning electron microscope direct-writing photoetching system comprises an electron chamber, an ion chamber, a sample chamber and a control system; the electron chamber comprises an electron chamber cavity, an electron gun, an anode, an electron beam blocker, an electromagnetic lens and an electron beam deflection coil; the ion chamber comprises an ion chamber cavity, an ion source, an ion beam scanning deflection electrode and the like; the sample chamber comprises a sample chamber cavity, a secondary electron detector, a nano-precision flexible servo motion platform system and the like; the control system comprises a computer, an electron beam scanning controller, an ion beam scanning controller and the like. The electron beam generated by the electron chamber or the ion beam generated by the ion chamber can be used for nano direct-writing preparation, and the nano-precision flexible motion platform in the sample chamber and the electron beam / ion beam can cooperatively move or be linked, so that splicing errors in preparation are avoided, and large-area nano direct-writing photoetching without splicing errors is realized. The system can also perform in-situ detection in the preparation process, so that the preparation result is convenient to observe in real time.