When serving in extremely high-power laser conditions, KH₂PO₄ (KDP) surfaces are susceptible to incur laser damage points (also known as defects). Using micro-ball end milling cutters to repair and remove the pre-existing damage points on the flawed KDP crystal surface is the most effective method to control the growth of laser damage points on KDP crystal surfaces and prolong their service life. However, there are various forms of micro-defects (such as pits, scratches and brittle fractures) around the laser damage points on KDP crystal surfaces which possess remarkable effects on the micro-milling repair process and consequently deteriorate the repair quality. In this work, combined with nano-indentation experiments, elastic–plastic mechanics and fracture mechanics theory, a constitutive model considering the anisotropic property of KDP crystals and a three-dimensional (3D) finite element model (FEM) were established to simulate the cutting force and surface topography involved in the ball-end milling repairing of flawed KDP crystal surfaces. Besides, the micro-milling experiments were conducted to evaluate the change of cutting force and machined surface quality in the presence of micro-defects with various feed rates. The results show that micro-defects would induce the fluctuation of cutting force and a change of the undeformed cutting thickness (UCT) in the process of repairing the damage points on the crystal surface, which would lead to the brittle–ductile transition (BDT) and affect the machined surface quality. The machined surface quality was found to be deteriorated by the pre-existing micro-defects when the UCT was small (the UCT was less than 375 nm). On the contrary, brittle mode cutting in the local area can be transformed into ductile mode cutting, resulting in an improvement of repaired surface quality that is exhibited by the cutting force and microtopography. This work has great theoretical significance and engineering practical value for the promotion and application of micro-milling repairing technology in the practical manufacturing and operation of KDP optics applied to high-power laser systems.