Objective To investigate the effect of Shenqi Yizhi Granules on brain structure and function in prodromal Alzheimer disease（pAD） under hypoxic conditions based on MRI. Methods A total of 77 female Han Chinese patients， aged 50‒85 years， who had at least 6 years of education and long-term residence in Qinghai region and met the inclusion criteria for pAD were enrolled as subjects. They were randomly divided into drug group （39 patients receiving Shenqi Yizhi Granules） and control group （38 patients receiving placebo） for 24 weeks of clinical observation. Related data were collected from all subjects， including clinical information， cognitive and neuropsychological assessments， diffusion tensor imaging （DTI） data， and rs-fMRI data. Results Cognitive and neuropsychological assessments showed that after treatment， the drug group had significant increases in MoCA， AVTL， SDMT， and CFT-copy scores and significant reductions in ADAS-cog and GDS scores（P<0.05）， while the control group had a significantly increase in ADAS-cog score （P<0.001）； compared with the control group after treatment， the drug group had significantly higher MoCA and AVTL scores （P<0.05） and a significantly lower ADAS-cog score （P<0.01）. DTI results showed that the drug group had significant increases in axial diffusivity （AD） values of multiple brain regions after treatment （P<0.05）. The results of rs-fMRI showed that after treatment， the drug group had significant increases in the amplitude of low-frequency fluctuation （ALFF） in the right temporal middle gyrus， the triangular part of the inferior frontal gyrus， and the medial cingulate gyrus and paracingulate gyrus and significant reductions in ALFF in the left cerebellar hemisphere Crus1 lobule， superior occipital gyrus， and supramarginal gyrus， and compared with the control group， the drug group had a significant increase in ALFF in the right dorsolateral superior frontal gyrus （P<0.05）. After treatment， the drug group had significant increases in the regional homogeneity （ReHo） values of the left triangular part of the inferior frontal gyrus and the inferior occipital gyrus and a significant reduction in the ReHo value of the left cerebellar hemisphere Crus1 lobule （P<0.05）， and compared with the control group， the drug group had a significant increase in the ReHo value of the left inferior parietal gyrus（P<0.05）. Conclusion Shenqi Yizhi Granules can effectively improve overall cognition and the function of multiple cognitive domains in pAD patients living in plateau regions by modulating the microstructure of white matter and spontaneous neuronal activity in cognitive-related brain regions.