Infrared micro-optics arrays (MOAs) featuring large numbers of micro-freeform lenslet are required increasingly in advanced infrared optical systems. Ultra-precision diamond cutting technologies have been widely used to fabricate MOAs with high form accuracy. However, the existing technologies can easily cause the non-uniformly fractured surface of infrared MOAs, due to the inherent low fracture toughness and high anisotropy of infrared materials as well as the time-varying chip thickness induced by ever-changing height and slope of the desired MOAs. In this study, a novel self-tuned diamond milling (STDM) system is proposed to achieve the ductile cutting of infrared MOAs with enhanced the surface uniformity and machining efficiency, and the corresponding toolpath planning algorithm is developed. In STDM system, a dual-axial fast servo motion platform is integrated into a raster milling system to self-adaptively match the maximum chip thickness for each tool rotational cycle with the critical depth of cut of the infrared material according to the local surface topography, thereby obtaining crack-free lenslet with high surface uniformity. Practically, micro-aspheric MOAs free from fractures are successfully machined on single-crystal silicon, a typical infrared material, to validate the proposed cutting concept. Compared with the conventional diamond milling, the proposed STDM is demonstrated to be able to avoid the non-uniform fractures without needing to reduce feed rate, and a smaller surface roughness of 4 nm and nearly double machining efficiency are achieved.