Femtosecond laser direct writing (FsLDW) has been widely applied in the field of mico-nano fabrication for its advantages such as excellent three-dimensional processing ability, high spatial resolution and low additional damage. However, there are contradictions between machining efficiency, machining area and machining accuracy in the conventional FsLDW. In order to realize high speed, large area and high precision in the process of laser micro-nano fabrication, we have built a new FsLDW system based on polar coordinates, which is composed of large scale horizontal linear stages and high speed rotary stage. The approaches for the alignment of axisymmetric sample′s center and the calibration of surface curvature have been investigated based on the proposed system, and a multilevel three-dimensional structure has been fabricated on a curved surface. Finally, a diffractive circle grating structure with diameter of 10 mm has been fabricated on curved surface of the lens, and the femtosecond laser fabrication of large area three-dimensional structure with high speed, large scale and high precision has been realized. The research provides strong technical support for the fabrication of high performance hybrid refractive-diffractive optical element.