Despite the complex geometry of songbird's vocal system, it was typically modelled as a tube or with simple mathematical parameters to investigate sound filtering. Here, we developed an adjustable computational acoustic model of a sparrow's upper vocal tract ( Passer domesticus ), derived from micro-CT scans. We discovered that a 20% tracheal shortening or a 20° beak gape increase caused the vocal tract harmonic resonance to shift toward higher pitch (11.7% or 8.8%, respectively), predominantly in the mid-range frequencies (3–6 kHz). The oropharyngeal-oesophageal cavity (OEC), known for its role in sound filtering, was modelled as an adjustable three-dimensional cylinder. For a constant OEC volume, an elongated cylinder induced a higher frequency shift than a wide cylinder (70% versus 37%). We found that the OEC volume adjustments can modify the OEC first harmonic resonance at low frequencies (1.5–3 kHz) and the OEC third harmonic resonance at higher frequencies (6–8 kHz). This work demonstrates the need to consider the realistic geometry of the vocal system to accurately quantify its effect on sound filtering and show that sparrows can tune the entire range of produced sound frequencies to their vocal system resonances, by controlling the vocal tract shape, especially through complex OEC volume adjustments.