Hypobaric hypoxia (HH) is a typical characteristic of high altitude environment and causes a spectrum of pathophysiological effects, including headaches, gliovascular dysfunction and cognitive slowing. Here, we sought to understand the mechanisms underlying cognitive deficits under HH exposure. Our results showed that HH exposure impaired cognitive function and suppressed dendritic spine density accompanied with increased neck length in both basal and apical hippocampal CA1 region neurons. The expression of PSD95, a critical synaptic scaffolding molecule, is down-regulated by hypoxia exposure and post-transcriptionally controlled by cold-inducible RNA-binding protein (Cirbp) through 3’-UTR region binding. PSD95 expressing alleviates hypoxia-induced neuron dendritic spine plasticity abnormality and memory impairment. Moreover, overexpressed Cirbp in hippocampus rescues hypoxia-induced loss of PSD95 and attenuates hypoxia-induced dendritic spine injury and cognitive outcomes. Thus, our findings reveal a novel mechanism where Cirbp-PSD-95 axis appears to play a key role in hypoxia-induced cognitive abilities impairment in brain.