Sleep deprivation (SD) disrupted subcortical regions involved in emotion and attention. However, the age-related changes on subcortical brain morphology in processing of emotion and attention following SD remains unclear. Eighty participants consisting of 43 young people and 37 old people were included in this study. The volumetric analysis and vertex-wise shape analysis were employed to assess age-dependent structural abnormalities after SD. By volumetric analysis, we found significant main effect of deprivation with local atrophy in right amygdala. Shape analysis also showed the significant main effect of age in all subcortical structures. Moreover, the significant correlations between volume changes of bilateral amygdala and left thalamus after SD and scales scores refer to emotion processing and attention were observed in old adults. These findings indicated that SD altered gray matter volume and surface morphology of subcortical regions in old adults and suggested disrupted subcortical regions were associated with emotion and attention in old adults.