Environmental factors may influence brain iron concentration. We investigated the changes of magnetic susceptibility and R2* values of cerebral regions especially in six deep gray matter nuclei of twenty-nine participants after high altitude exposure for four weeks. The results show that the susceptibility values of gray matter, especially in caudate nucleus, putamen, globus pallidus, substantia nigra, red nucleus, increased significantly. Traditional R2* maps verify the results of QSM evaluation except in red nucleus. Therefore, high altitude hypoxia can lead to significant increase of cerebral iron concentration.