The reconstruction of the three-dimensional structure of the nasal cavity is significant for the diagnosis and treatment of nasal and nasopharynx diseases. This study proposes a method for reconstructing the three-dimensional structure of the nasal cavity based on the short-source acoustic tube, which addresses the inconvenient portability and high cost of the long-source acoustic tube. Firstly, we separate incident and reflected waves based on the propagation characteristics of pulsed acoustic waves in a short-source acoustic tube. Secondly, to reduce the error in calculating the input impulse response sequence, the methods of correcting the direct current (DC) offset component and suppressing the high-frequency noise are used to pre-process the nasal acoustic signals. Finally, we adopt the layered reconstruction method of the three-dimensional structure of the nasal cavity to reconstruct the depth cross-sectional area two-dimensional curve and take a three-dimensional visualization. Through comparative analysis, this method can meet practical application requirements.