The fabrication of micro-holes in hard-to-machine materials presents considerable challenges in precision machining. This study proposes a novel approach that employs high-strength micro-grinding tools with a central abrasive grain absence to create micro-holes through helical grinding. Due to the random distribution of abrasive grains, the absence of grains at the tool’s center becomes an inevitable technical challenge. This research examines the correlation between the diameter of the absence zone and the bottom morphology of the machined hole, highlighting the potential formation of disc-shaped or cylindrical residues. A model for predicting the height of the disc-shaped residues is developed, and the mechanisms governing their removal during grinding are further explored. The findings indicate that when a central grain absence exists, the first abrasive grain surrounding the absence zone, referred to as the inner-edge grain, is responsible for removing the disc-shaped residues. Based on these results, a novel 0.8 mm diameter micro-PCD milling–grinding tool with a central edge absence is designed, and experimental validation is performed using 65% SiCp/Al composite materials. The experimental results confirm that the central grain absence leads to the formation of disc-shaped residues at the bottom of the machined hole during helical grinding, and the morphology of the experimentally obtained residues aligns with the theoretical predictions and simulations. This study significantly advances micro-grinding wheel technology and provides a solid foundation for the precision machining of micro-holes in hard-to-machine materials.