Micro-holes are channels for signal connection between layers of printed circuit boards (PCBs), and excess invalid hole copper in through holes can destroy the integrity of signal, which is usually removed by back-drilling. However, as high-speed PCBs evolve towards miniaturization and high density, it is difficult to remove chips during back-drilling and easily cause micro-holes plugging, seriously affecting the performance of high-speed PCBs and even leading to scrap. Therefore, the chip removal mechanism of high-speed PCB back-drilling is studied to solve hole plugging in this paper. Firstly, kinematics method is used to analyze the mechanical behavior and motion law of chip formation, and then the expressions of chip removal force and chip moving speed are proposed. Secondly, the chip removal model of backdrilling is established, an evaluation index of chip removal capability is put forward, and the influence rule of machining parameters on chip removal of back-drilling is analyzed afterwards. Finally, back-drilling experiments of high-speed PCB are carried out to observe the chips winding around drill bit and calculated the hole plugging rate of back-drilling. The experimental result demonstrates that the number and density of winding chips in the drill bit slightly decrease with the increase of feed rate, and the hole plugging rate rises almost proportionally. Increasing the spindle speed can greatly improve the chip winding of tools and hole plugging, and effectively reduce the chip removal force of back-drilling. The research presented provides theoretical guidance for solving the bottleneck problem of micro-holes plugging during backdrilling in the high-speed PCB industry.