Laser-induced damage points (known as defects) would seriously reduce the service life of large-aperture KDP optics in high-power laser devices. The ball-end milling procedure is recognized as an efficient method for creating a Gaussian mitigation pit (GMP) to restore the optical transmission performance of functional KDP crystals by removing defects. Nevertheless, achieving smooth and flawless Gaussian curved microstructures is a massive challenge for soft-brittle KDP crystals. Herein, a judging criterion of the ductile-regime machining for the GMP is developed by the models of uncut chip thickness (UCT) and critical milling depth. Simultaneously, the obtained judging criterion can be validated by the microstructure fabrication experiments. Besides, considering the spindle vibration, plowing effect, and machined surface texture, the influence of spindle speed (n), feed rate (f), and tool mark interval (d) on the surface formation mechanism of the GMP is analyzed, respectively. It can be discovered that the n of up to 60,000 r/min can lead to severe velocity fluctuation of the motion system, increasing the UCT and causing brittle fractures on the KDP surface. A low f can result in an undesirable plowing phenomenon, and a large number of crystal materials are accumulated in the up-cut process. Once the f reaches 72 mm/min, the tool path would fluctuate significantly, resulting in poor GMP surface texture. When the d exceeds 15 μm, the surface quality of the GMP can no longer meet the engineering requirements of the Ra ≤ 50 nm. Moreover, the optimized processing parameters of the microstructure fabrication are 47,800 r/min in the n, 30 mm/min in the f, and 5 μm in the d. This study can provide crucial guidance for obtaining the ultra-smooth and defect-free GMP processed in the ductile regime, which would resultantly possess significant theoretical importance and practical value in enhancing the optical properties of flawed KDP crystals.