The unique microstructures of bulk metallic glasses (BMGs) provide them with excellent mechanical, physical, and chemical properties, having important applications in the fields of medical devices, military equipment, aerospace, etc. However, the superb mechanical properties also contribute to poor machinability of the BMGs. Currently, researchers have proposed to improve the machinability by single-point diamond turning, laser-assisted machining and ultrasonic vibration-assisted machining, but their plasticity and viscous flow remain unchanged, thus restraining further enhancement of surface quality. Atmospheric pressure cold plasma jet (APCPJ), which is rich in active particles, can effectively ameliorate material machinability by modulating material properties. In this paper, we propose to use the APCPJ to regulate the properties of BMGs, and carry out nanoindentation, nanoscratching, and micro-milling experiments to investigate the influence mechanisms of APCPJ on the material properties and cutting process. The results demonstrate that after modified by APCPJ, plastic deformability of the BMGs is improved due to the increase of free volume content; meanwhile, the viscous flow is inhibited. The micro-milling experiments indicate that under the conditions of feed rate Vf = 500 μm/s, spindle speed n = 30,000 rpm, and cutting depth ap = 5 μm, the improvement effect of APCPJ on the cutting process is relatively optimum. The surface roughness Ra of the Zr-based BMG and Ti-based BMG obtained by APCPJ are respectively 0.076 μm and 0.081 μm, which can be reduced by 37.7 % and 38.2 % compared with dry micro-milling. The cutting forces Fz in the direction of cutting depth are also reduced by 30.9 % and 23.3 %, respectively. The APCPJ-assisted micro-milling method proposed in this work may ameliorate the machining quality of BMGs and promote the application of BMGs and APCPJ-assisted machining technology in aerospace and precision machining.