We demonstrated a new method to fabricate micron-sized grooves with high aspect ratios in silicon wafers by combining femtosecond laser irradiation and oxygen-dependent acid etching. Femtosecond laser was employed to induce structure changes and incorporate oxygen into silicon, and then materials in oxygen-containing regions were etched by hydrofluoric acid (HF) solution to form grooves. The etching could be attributed to the reaction between HF and silicon oxides formed by femtosecond laser irradiation. The dependences of the aspect ratios of grooves on the laser fluence and the scanning velocity were also investigated.