In this study, hydride vapor phase epitaxy (HVPE), one of the feasible methods to produce the GaN thin film, has been used to conduct experiments under different temperatures. In order to study the factors affecting the distribution of the density of the hillocks along radial direction, we have conducted a 3D calculation to observe the fluid flow, mass transfer and deposition rate distribution using the CFD-ACE program. The numerical results have shown that the wafers have experienced high and low growth rate alternately. The growth rate fluctuations at different distances from the inlets are compared by standard deviation analysis. These standard deviations of deposition rates along the azimuthal direction increase from the center to the periphery, which might explain why the density of the hillocks increases from the center to the periphery in the experiments. Moreover, it is found that the non-uniform deposition rates are the result of low speed rotation of the susceptor. Increasing the rotation speed of the susceptor increases the uniformity of the gas flow pattern and deposition rate, which means that the high rotation speed can decrease the standard deviation of the deposition rate along azimuthal direction. Consequently, the density of the hillocks can be decreased.