The human whistle is a typical aeroacoustic sound. Downstream of a small orifice made by the lips, a jet is formed by airflow with a high Reynolds number. A sequence of vortex rings is then produced, and periodic air pressure changes result in a characteristic whistling sound. Although the vocal tract has been reported to act as an acoustic resonator determining the blowing pitch, the precise shape of the vocal tract and its resonance properties during whistling remain unclear. In the current study, the morphological and acoustic properties of the vocal tract were examined during the act of whistling in a single participant. The vocal tract was scanned in three dimensions using magnetic resonance imaging while four musical notes were produced. The data revealed that the tongue constricted the vocal tract in different ways depending on the note, and the location of the constriction moved forward when the blowing pitch increased. Acoustic analysis of the vocal tract showed that the second peak of the lip input impedance was largely in accord with the whistling pitch. In addition, specific regions in the vocal tract were highly acoustically sensitive to small deformations.