Hot embossing is an efficient technology for the fabrication of glass micro- and nanostructures. However, the long cycle time, high energy consumption, and high nitrogen emissions in traditional hot embossing approach hinders sustainable production of glass micro-optics. Therefore, this paper proposes a novel two-stage gravity-assisted hot embossing process that enables the fabrication of high-quality glass micro-pillar arrays in a rapid, green manner. In this approach, the two-stage gravity loading unit provides accurate force on glass preform through a simple control system, and the tailor-made heating module based on Si3N4 ceramic heaters requires an energy consumption of just 700 kJ per molding cycle. As a result, the proposed approach is featured by low energy consumption and high manufacturing efficiency. In this study, the effects of the embossing temperature, force, and time on the replication accuracy of a K9 glass micro-pillar array were investigated through a series of hot embossing experiments. Afterward, the form accuracy, uniformity of microstructures, and warpage of glass replicas under the optimal process parameters were evaluated separately. Finally, repeated hot embossing experiments were conducted to demonstrate the reproducibility of the hot embossing process. The experimental results show that embossing temperature had the most significant effect on the replication accuracy of glass micro-pillars. By optimizing the process parameters, the embossed glass micro-pillars could achieve transfer ratios of 99.00% and 95.14% in height and diameter, respectively. Moreover, the surface roughness of glass micro-pillars was less than 5 nm, and the warpage amplitude of glass replicas in a 3.9 × 3.9 mm area was smaller than 1 μm. The small discrepancy in geometric features of glass replica in the repeated trails reflects the satisfactory reproducibility of this hot embossing process on the micro and nano scales. The results indicate the strong industrialization potential of the proposed two-stage gravity-assisted hot embossing machine and hot embossing process for fabricating high-quality glass microstructures more cleanly and sustainably.