Three-dimensional acoustic impedance microscopy was proposed for human cheek skin observation. A focused ultrasound wave was transmitted through a polymer substrate in contact with the skin, and the reflection was acquired by a time-domain measurement. The reflection was compared with that from a reference material representing the impulse response of the system. Time-frequency (dual-domain) deconvolution was performed to calculate the time-dependent reflection coefficient, which can subsequently be interpreted as the local acoustic impedance along the depth. The optimal conditions for deconvolution were discussed in order to perform quick and stable signal processing. Moreover, it was found that the stability of the dual-domain deconvolution was improved by adding the DC component to the transfer matrix, leading to a more stable calculation of the acoustic impedance distribution. The stability was statistically evaluated by means of the intensity distribution of the deconvolved signal. Finally, a 3D human cheek skin image was successfully reconstructed.