An Atomic Force Microscope (AFM) system with high-speed and large-area was constructed to measure the micro-structure surface of an optical grating. The effects of scanning speed on measuring results under different scanning modes were researched. First, the spectra of the micro-probe under constant-height and constant-force modes were measured, respectively, and the effective bandwidths of the probe were obtained under the two modes. Then, based on the constant-height and constant-force modes, the effects of scanning speed on measuring results were analyzed via measuring a line and a circle on the surface of the optical grating at different scanning speeds. By employing this AFM system, the 3-dimensional profile of the large-area micro-structure surface on the optical grating was measured at a distortionless scanning-speed in a constant-height mode. The results show that it takes only 40 s to measure a circle area with a diameter of 40 mm on the grating surface. When the scanning speed is no more than the speed that is corresponding to the effective bandwidth of the micro-probe, the AFM system can achieve the high-speed, large-area and distortionless measurement for micro-structure surfaces.