In this study, methane–ethylene jet diffusion flames modulated by acoustic excitation in an atmospheric environment were used to investigate the effects of acoustic excitation frequency and mixed fuel on nanomaterial formation. Acoustic output power was maintained at a constant value of 10 W, while the acoustic excitation frequency was varied (f = 0–90 Hz). The results show that the flame could not be stabilized on the port when the ethylene volume concentration (ΩE) was less than 40% at f = 10 Hz, or when ΩE = 0% (i.e., pure methane) at f = 90 Hz. The reason for this is that the flame had a low intensity and was extinguished by the entrained air due to acoustic modulation. Without acoustic excitation (f = 0 Hz), the flame was comprised of a single-layer structure for all values of ΩE, and almost no carbon nanomaterials were synthesized. However, with acoustic excitation, a double-layer flame structure was generated for frequencies close to both the natural flickering frequency and the acoustically resonant frequency. This double-layer flame structure provided a favorable flame environment for the fabrication of carbon nanomaterials. Consequently, the synthesis of carbon nano-onions was significantly enhanced by acoustic excitation near both the natural flickering frequency and the acoustically resonant frequency. At f = 20 Hz (near the natural flickering frequency) for 0% ≤ ΩE ≤ 100%, a quantity of carbon nano-onions (CNOs) piled like bunches of grapes was obtained as a result of improved mixing of the fuel with ambient air. High-density CNOs were also produced at f = 70 Hz (close to the acoustically resonant frequency) for 40% ≤ ΩE ≤ 100%. Furthermore, carbon nanotubes (CNTs) were synthesized only at 80 Hz for ΩE = 0%. The suitable temperature range for the synthesis of CNTs was slightly higher than that for the formation of CNOs (about 600 °C for CNTs; 510–600 °C for CNOs).