The drilling of printed circuit board (PCB) using micro-drills is an important processing method in modern industry. A protective film with good lubricating and anti-wear properties is generally applied to improve the processing problems of micro-drills during operation. In this study, the effects of C2H2 flow rate on the microstructure, mechanical, and tribological properties of a-C:H films deposited by plasma enhanced chemical vapor deposition (PECVD) technique were investigated. The results showed that when the C2H2 flow rate was low, varying the flow rate had little effect on the microstructure of the prepared a-C:H films. However, when the C2H2 flow rate was greater than 210 sccm, the increase in flow rate caused large particles of carbon clusters to aggregate on the surface of a-C:H films, which resulting in an increase Ra value. Not only did it reduce the adhesion between the film and the substrate, but it also deteriorated the mechanical and tribological properties of the a-C:H film produced. In addition, a-C:H films were also deposited on the micro-drill, and were used for drilling tests on the PCBs to evaluate its servce capability. The optimal parameters of a-C:H film deposited on the micro-drill surface were obtained by observing the morphology of the micro-drill surface after drilling and the hole accuracy statistics. The results showed that a-C:H film deposited on the surface of the micro-drill showed the best machining performance when the C2H2 flow rate was 180 sccm. The surface wear of micro-drill was minimal, the entanglement of tangled chips was minimal. The value of the process capability index (CPK) after 500, 1000, and 2000 drilling of PCB boards was 5.95, 4.33, and 3.15 respectively, which showed the highest drilling accuracy. This is mainly attributed to the better overall properties of the a-C:H films prepared at C2H2 flow rate of 180 sccm, such as lower surface roughness, lowest residual stress, higher hardness, better adhesion, and lower friction coefficient.