Work-piece elastic deformation caused by clamping force from fixture will lead to part bending or distorting, which is critical to lower its quality performance. In this paper, a novel zonal compensation method is proposed to compensate the work-piece elastic deformation through fixture layout optimization based on High Definition Metrology (HDM). The zonal surface flatness data of work-piece in fixture is obtained with densely optical measurement firstly. Then, they are reorganized according to the accuracy requirement based on the zonal distribution. Finally, the surface flatness compensation model based on fixture layout is made. The practicality and effectiveness of this new approach was verified using the case of Aluminum alloy 6061 part milling.