As a common structure, microholes are widely used in various fields, including biomedical, aerospace, 3D packaging and so on. Femtosecond laser has unique advantages in drilling high-quality microhole due to its ultra-short pulse duration and ultra-high peak power. This review covers temporally/spatially shaped femtosecond laser microhole drilling methods and their applications over the past decade, including femtosecond laser temporally/spatially shaped methods, temporally/spatially shaped femtosecond laser microhole drilling based on electrons dynamics control, and the applications of microhole in transmittance enhancement and anti-reflection, material cutting, oil/water separation, fog collection and gas collection. Furthermore, present challenges and future research opportunities in this field are analyzed.