A time-resolved shadowgraphic imaging system based on femtosecond laser pump and probe is established for directly imaging the ultrafast process of femtosecond laser ablating of micro-holes in silica glass. The time-delay dependent phenomena of plasma channel decay, shock wave expansion, and micro-hole stretch are observed when the energy density, time-delay, and pulse number change. The experimental results show that the proposed system is very efficient for the in situ observation of the micro-nanostructures in transparent media induced by femtosecond laser ablation.