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The formation and distribution of residual stress during the micro-milling process significantly affect the crack resistance and service life of alumina bioceramics. This study aims to optimize the surface residual stress distribution by adjusting machining parameters, thereby improving the machining quality of alumina ceramics. A three-dimensional finite element model of alumina bioceramics was developed, and numerical simulations were conducted to analyze the effects of feed per tooth, cutting depth, and spindle speed on temperature and residual stress. The study further explores the patterns of residual stress variation. The results show that both surface temperature and residual tensile stress exhibit systematic trends with parameter changes. Specifically, surface residual tensile stress increases with cutting depth initially but decreases sharply once the cutting depth exceeds 25 μm. Residual tensile stress increases with spindle speed, reaching its peak at 21,000 r/min before stabilizing. Additionally, the residual tensile stress rises with feed per tooth at first but gradually declines when the value exceeds 25 μm/z. This research reveals the mechanisms by which micro-milling parameters influence surface temperature and residual stress in alumina bioceramics, providing theoretical guidance for optimizing micro-milling processes. The findings can also be extended to the micro-milling of other hard-to-machine materials, offering broad engineering application potential.