AbstractDepression is a significant concern among astronauts, yet the molecular mechanisms underlying spaceflight‐induced depression remain poorly understood. MicroRNAs (miRNAs) have emerged as potential regulators of neuropsychiatric disorders, including depression, but their specific role in space‐induced depression remains unexplored. This study aimed to elucidate the involvement of candidate miRNAs (miR‐455‐3p, miR‐206‐3p, miR‐132‐3p, miR‐16‐5p, miR‐124‐3p, and miR‐145‐3p) and their interaction with differentially expressed genes (DEGs) in the neurobiology of spaceflight‐induced depressive behavior. Using a simulated space environmental model (SCSE) for 21 days, depressive behavior was induced in rats, and candidate miRNA expressions and DEGs in the cortex region were analyzed through qRT‐PCR and HPLC, respectively. Results showed that SCSE‐exposed rats exhibited depressive behaviors, including anhedonia, increased immobility, and anxiousness compared to controls. Further analysis revealed increased hydrogen peroxide levels and decreased superoxide dismutase levels in the SCSE group, indicating abnormal oxidative stress in the cerebral cortex. Moreover, miRNA analysis demonstrated significant upregulation of miR‐455‐3p, miR‐206‐3p, miR‐132‐3p, and miR‐16‐5p expression. Among the DEGs identified, the in silico analysis highlighted their involvement in crucial pathways such as glutamatergic signaling, GABA synaptic pathway, and calcium signaling, implicating their role in spaceflight‐induced depression. Protein–protein interaction analysis identified hub genes, including DLG4, DLG3, GRIN1, GRIN2B, GRIN2A, SYNGAP1, DLGAP1, GRIK2, and GRIN3A, impacting neuronal dysfunction functions in the cortex region of SCSE depressive rats. DLG4 emerged as a core gene regulated by miR‐455‐3p and miR‐206‐3p. Overall, this study underscores the potential of miRNAs as biomarkers for mood disorders and neurological abnormalities associated with spaceflight, advancing health sciences, and space health care.