The surface with micro-dimpled structures on the target ball is helpful for improving nuclear fusion efficiency in inertial confinement fusion. Micro ball-end milling with copying method can provide a simple and effective option in machining micro dimples with high surface finish and geometry (dimension and shape) accuracy. In this paper, based on the established geometric error model, the influence of geometric errors and structural parameters of the machine tool on the dimple dimension and shape was first studied. Next, a model expressing the trajectory of cutting edge for simulating dimple geometry generated by ball-end milling was built. The model was used to analyze the effect of the spindle attitude, tool run-out and deflection deformation on the dimple dimension and shape. Micro ball-end milling tests were carried out, and the dimension, shape and cross-section profile of simulated and milled dimples were compared. A good correspondence between the simulated and milled dimple was observed, the largest error is 6.87%. Finally, from surface morphologies and surface roughness of the milled dimples, it was found that spindle attitude, axial feed rate are the main factors affecting the surface quality of micro dimple machined using micro ball-end milling with copying method. In particular, the axial feed rate need being optimized, reducing the effect of cutting edge quality and avoiding the deterioration of dimple surface and contour caused by a high feed rate. This research is of great significance for fabricating micro-dimpled functional surfaces by surface texturing based on milling methods.