An ultra-precision machining system includes a worktable, a first support device, a second support device, a rotating shaft, a cutting tool, a detector and a controller. The first support device is fixed on the worktable. The second support device is movably mounted on the worktable. The rotating shaft is rotatably connected to the first support device. The cutting tool is mounted on the second support device and is movable relative to the second support device along a vertical direction. The detector is fixedly connected to the first support device above the rotating shaft for detecting an axial deviation of the rotating shaft. The controller is configured for calculating the axial deviation of the rotating shaft and adjusting the position of the cutting tool relative to the rotating shaft to counteract the calculated axial deviation of the rotating shaft.