Volatile methyl siloxanes (VMSs) as a trace impurity in biogas decreases its energy utilization, and thus need to be removed. In this paper, a one-step hydrothermal reduction was performed to produce three-dimensional reduced graphene oxide aerogels (rGOAs) using industrial-grade graphene oxide (IGGO) as raw material and vitamin C (VC) as a reductant to facilitate the fabrication of rGOAs. The synthesis of rGOAs was a simple, green, and energy-efficient process. The developed rGOAs were characterized using the Brunauer–Emmett–Teller method, Raman spectrometry, scanning electron microscopy, Fourier-transform infrared spectroscopy, X-ray diffraction measurements and contact angle. The results obtained showed that rGOA-1 with a VC/IGGO ratio of 1/1 (m/m) exhibited a hierarchical porous structure and super-hydrophobicity, yielding a high specific surface area (137.9 m2 g−1) and superior water contact angle (143.8°). The breakthrough adsorption capacity of rGOA-1 for hexamethyldisiloxane (L2, a VMS model) was 11 times higher than that of IGGO. Low inlet concentration and bed temperature were considered beneficial for the L2 adsorption. Interestingly, rGOA-1 was less sensitive to water, and it was readily regenerated for reuse by annealing at 80 °C. The rGOAs have been demonstrated to have great potential for the removal of siloxanes from biogas.