The nasal cavity three-dimensional structure reconstruction is significant for the diagnosis and treatment of nasal and nasopharynx diseases. Currently, most systems for nasal cavity three-dimensional structure reconstruction are based on a long-source acoustic tube. However, the long-source acoustic tube has the weaknesses of low portability and high cost. To address these issues, a nasal cavity three-dimensional structure reconstruction system based on a short-source acoustic tube was designed in this research. The designed system comprises the lower computer of a nasal acoustic signal acquisition device and the upper computer of nasal acoustic signal analysis software. The lower computer of a nasal acoustic signal acquisition device consists of a signal processing unit, a detection unit, a microcontroller, and a USB communication interface. It is used to collect the original acoustic signal in the nasal cavity. The upper computer of nasal acoustic signal analysis software consists of the nasal cavity acoustic signal preprocessing method and the nasal cavity three-dimensional structure hierarchical reconstruction method. The nasal cavity acoustic signal preprocessing method is used to eliminate the DC offset component and suppress the high-frequency noise. Then, the nasal cavity three-dimensional structure hierarchical reconstruction method is used to establish the relationship between the cross-sectional area of the nasal cavity and the depth of the nasal cavity. In order to verify the effectiveness of the system designed in this research, the straight tube model and the simulated nasal cavity model were selected as test subjects, and the depth–cross-sectional area was selected as the evaluation indicator of the accuracy of the nasal cavity three-dimensional structure reconstruction result. The experimental results show that the root mean squared error and the mean relative error of the depth–cross-sectional area were reduced from 0.6284 cm2 to 0.0201 cm2 and 47.6467% to 1.8248%, respectively, under the straight tube model by using the nasal cavity acoustic signal preprocessing method. The root mean squared error and the mean relative error of the depth–cross-sectional area were reduced from 4.7730 cm2 to 0.1510 cm2 and 107.8128% to 3.3096%, respectively, under the simulated nasal cavity model. Meanwhile, this system can increase the effective measurement depth of the nasal cavity from 7 cm to 13 cm based on the preprocessing method. The results demonstrated that the designed system can not only reconstruct and visualize a nasal cavity three-dimensional structure with high precision but also generate comprehensive test reports. Therefore, this system can provide a basis for further auxiliary diagnosis of the disease and facilitate doctors in explaining the physiological structure of the nasal cavity to patients.