High-aspect-ratio microholes, the fundamental building blocks for microfluidics, optical waveguides, and other devices, find wide applications in aerospace, biomedical, and photonics fields. Yttrium aluminum garnet (YAG) crystals are commonly used in optical devices due to their low stress, hardness, and excellent chemical stability. Therefore, finding efficient fabrication methods to produce high-quality microholes within YAG crystals is crucial. The Bessel beam, characterized by a uniform energy distribution along its axis and an ultra-long depth of focus, is highly suitable for creating high-aspect-ratio structures. In this study, an axicon lens was used to shape the spatial profile of a femtosecond laser into a Bessel beam. Experimental verification showed a significant improvement in the high aspect ratio of the microholes produced in YAG crystals using the femtosecond Bessel beam. This study investigated the effects of the power and defocus parameters of single-pulse Bessel beams on microhole morphology and size, and microhole units with a maximum aspect ratio of more than 384:1 were obtained. Based on these findings, single-pulse femtosecond Bessel processing parameters were optimized, and an array of 181 × 181 microholes in a 400 μm thick YAG crystal was created in approximately 13.5 min. The microhole array had a periodicity of 5 μm and a unit aspect ratio of 315:1, with near-circular top and subface apertures and high repeatability.