A 3-D numerical simulation of a buried-channel CCD (Charge Coupled Device) with a deep depletion has been performed to investigate its electrical and physical behaviors. Results are presented for a deep depletion CCD (EEV CCD12; JET-X CCD) fabricated on a high-resistivity $(1.5kOmega-cm);65{mu}m$ thick epi-layer, on a $550{mu}m$ thick p+ substrate, which is optimized for X-ray detection. Accurate predictions of the Potential minimum and barrier height of a CCD Pixel as a function of mobile electrons are found to give good charge transfer. The depletion depth approximation as a function of gate and substrate bias voltage provided average errors of less than 6%, compared with the results estimated from X-ray detection efficiency measurements. The result obtained from the transient simulation of signal charge movement is also presented based on 3-Dimensional analysis.