An inverse temperature gradient is generally adopted in order to avoid second nucleation at the initial homoepitaxial growth due to O, C and H impurities. In this paper, we investigated the temperature distribution and mass transfer at the initial homoepitaxial AlN growth stage in a proprietary and fully automatic physical vapor transport sublimation reactor by FEMAG and an in-house finite element multi-phase mass transfer code, respectively. Homoepitaxial growth experiment was also conducted successfully based on numerical simulation results. The simulation and experiment results showed the deposition of O, C and H impurities at the initial homoepitaxial growth stage could be efficient avoided by an inverse temperature distribution. The crucible position played a key role on the temperature distribution and mass transfer during the subsequent AlN crystal growth stage. The numerical simulation results and successful homoepitaxial growth experiment placed a solid foundation for our future size enlargement growth experiments.