Micro-hole drilling is an important process for microfluidic device fabrication. Owing to its strong nonlinear absorption and‘cold’processing on materials, femtosecond laser is a promising tool for micromachining of glass. In the present study, effects of femtosecond laser parameters on hole drilling of silica glass are studied. The results show that both laser energy and processing speed affect the hole diameter and depth. When selecting proper parameters, long and straight micro-holes with no obvious crack and aspect ratio over 25∶1 can be obtained. Furthermore, in order to obtain better focusing-condition, the frequency doubling crystal beta-barium borate (BBO) is used to obtain 400 nm wavelength femtosecond laser. Compared with 800 nm wavelength, 400 nm femtosecond laser can get smaller hole diameter under the same focusing lens. Defects during femtosecond laser hole drilling are discussed as well.