In the present study, low energy ion implantation was employed to engineer the surface of a Zr-based bulk metallic glass (BMG), aiming at improving the biocompatibility and imparting bioactivity to the surface. Ca- or Ar-ions were implanted at 10 or 50 keV at a fluence of 8 × 10(15)ions/cm(2) to (Zr0.55Al0.10Ni0.05Cu0.30)99Y1 (at.%) BMG. The effects of ion implantation on material properties and subsequent cellular responses were investigated. Both Ar- and Ca-ion implantations were suggested to induce atom displacements on the surfaces according to the Monte-Carlo simulation. The change of atomic environment of Zr in the surface regions as implied by the alteration in X-ray absorption measurements at Zr K-edge. X-ray photoelectron spectroscopy revealed that the ion implantation process has modified the surface chemical compositions and indicated the presence of Ca after Ca-ion implantation. The surface nanohardness has been enhanced by implantation of either ion species, with Ca-ion implantation showing more prominent effect. The BMG surfaces were altered to be more hydrophobic after ion implantation, which can be attributed to the reduced amount of hydroxyl groups on the implanted surfaces. Higher numbers of adherent cells were found on Ar- and Ca-ion implanted samples, while more pronounced cell adhesion was observed on Ca-ion implanted substrates. The low energy ion implantation resulted in concurrent modifications in atomic structure, nanohardness, surface chemistry, hydrophobicity, and cell behavior on the surface of the Zr-based BMG, which were proposed to be mutually correlated with each other.