Damage to the visual cortex structures after high altitude exposure has been well clarified. However, changes in the neuronal activity and functional connectivity (FC) of the visual cortex after hypoxia/reoxygenation remain unclear. Twenty-three sea-level college students, who took part in 30 days of teaching at high altitude (4300 m), underwent routine blood tests, visual behavior tests, and magnetic resonance imaging scans before they went to high altitude (Test 1), 7 days after they returned to sea level (Test 2), as well as 3 months (Test 3) after they returned to sea level. In this study, we investigated the hematological parameters, behavioral data, and spontaneous brain activity. There were significant differences among the tests in hematological parameters and spontaneous brain activity. The hematocrit, hemoglobin concentration, and red blood cell count were significantly increased in Test 2 as compared with Tests 1 and 3. As compared with Test 1, Test 3 increased amplitudes of low-frequency fluctuations (ALFF) in the right calcarine gyrus; Tests 2 and 3 increased ALFF in the right supplementary motor cortex, increased regional homogeneity (ReHo) in the left lingual gyrus, increased the voxel-mirrored homotopic connectivity (VMHC) value in the motor cortex, and decreased FC between the left lingual gyrus and left postcentral gyrus. The color accuracy in the visual task was positively correlated with ALFF and ReHo in Test 2. Hypoxia/reoxygenation increased functional connection between the neurons within the visual cortex and the motor cortex but decreased connection between the visual cortex and motor cortex.