Bulk metallic glasses (BMGs) with amorphous structure have excellent mechanical and chemical properties. In polishing process, it is hard but important to maintain amorphous state to keep original properties of BMGs, which are easily crystallized in traditional mechanical polishing and long-pulse laser polishing. In this paper, we first propose to use femtosecond laser double-pulse irradiation to smooth the surface of Zr-based BMG and make it free of laser-induced periodic surface structures and crystallization. Here, the smooth surface with half decreasing in roughness (Sa) to 111 nm is achieved by optimized parameters with laser pulse energy 0.06 mu J of the first pulse, energy ratio 40% of the first to the second pulse and time delay 20 ps. Obvious transition from a coarse surface to a smooth one occurs at near 10 ps time delay and 40% energy ratio. Mobility enhancement of molten materials guarantees the removal of undesirable surface structures through surface tension and gravity. Crystallization is avoided due to rapid heating and cooling under femtosecond laser double-pulse irradiation. A smoothed BMG surface obtained by this method verifies its feasibility in BMGs polishing.