We studied the structural and elemental evolutions during the femtosecond laser percussion drilling of high-aspect-ratio diamond microholes. Microholes 225-μm-deep having an aspect ratio of 15 were drilled with an exposure time of 100 s and a laser power of 60 mW. It is found that when the specimen was machined by femtosecond laser at low power and short exposure time, the laser-affected zone (LAZ) may be still solid in the interior rather being void, even it reached the bottom of the diamond. A clear crack appeared between the solid portion and pristine diamond. Elemental analysis revealed that oxygen was incorporated into the solid portion of the LAZs, and its atomic percentage reached 6.5% for a laser power of 10 mW at initial position and decreased as the depth increased in the solid portion. The wall of the void contained nearly no oxygen. Furthermore, nanoripples were observed on the sidewall surface of the hole.