The alveolo-palatal sibilant fricative [ɕ] in /si/ and palatal non-sibilant fricative [ç] in /hi/ are known to be distinguished by the geometrical change of the vocal tract only in the coronal direction and acoustically unstable in some Japanese speakers. In this study, we reconstructed the vocal tract geometry with three repetitive magnetic resonance imaging (MRI) on the same subject and investigated the effects of coronal vocal tract shapes on the airflow and sound characteristics in [ç]. The computational grids were constructed on each vocal tract and a numerical airflow simulation was conducted to predict the turbulent airflow and aeroacoustic sound generation. The predicted sound properties were in good agreement with the measurement of Japanese subjects. The comparison of the airflow and acoustic characteristics among three vocal tracts showed that the slight changes of the constriction area and flow channel downstream from the constriction influenced the sound source generation and peak amplitudes at around 3 kHz, indicating that the characteristic peak of [ç] was variable due to the constriction shape at the middle part of the hard palate.