Frequency-dependent capacitance-voltage spectroscopy was applied to investigate the carrier transport dynamics in a silicon nanodots resonant tunneling device structure. Two negative differential resistance (NDR) regions in the current-voltage characteristics were found in this investigated structure. Two anomalous regions were also found in the capacitance-voltage spectroscopy, which coincide with the NDR regions in the current-voltage characteristics. The origin of the anomalous phenomenon was attributed to the mesoscopic quantum capacitance due to the holes transport through the energy states associated with the Si nanodots. An equivalent circuit model was proposed to quantitatively evaluate the frequency dependence of the capacitance-voltage spectroscopy.