Traumatic brain injury (TBI), particularly at high altitudes (HA-TBI), is a leading cause of mortality and disability, yet clear diagnostic and treatment protocols are lacking. This study explores the early pathophysiological changes occurring within 24 h following HA-TBI, with a focus on differentially expressed proteins (DEPs) and phosphorylated proteins (DEPPs). Using a low-pressure hypoxic chamber to simulate high-altitude conditions combined with a controllable cortical impact (CCI) model, we established a rat model of HA-TBI. Neurological function was evaluated using the modified Neurologic Severity Score (mNSS), while neuropathological and inflammatory responses following HA-TBI were evaluated through hematoxylin and eosin (HE) staining, immunofluorescence, Western blot (WB), and Enzyme-Linked Immunosorbent Assay (ELISA). In-depth proteomic and phosphoproteomic analyses were performed on the cerebral cortex at 6, 12, and 24 h post-injury. Bioinformatic analysis identified time-dependent DEPs, revealing dynamic changes in mRNA metabolism, ATP metabolism, and MAPK signaling during the early stages of HA-TBI. Common DEPs at 6, 12, and 24 h post-injury were linked to complement and coagulation cascades. Time-dependent DEPPs influenced synaptic structure and neurotransmission, with early changes in glutamatergic synapses being especially pronounced. Key pathways, including the complement and coagulation cascades and dopaminergic synapses, emerged as central to the injury response. Furthermore, proteins such as AHSG, APOA1, GRIN2B, phospho-GSK3β-S9, and CAMK2G were identified as critical regulators in these pathways. WB validated these findings, offering new insights into the mechanisms underlying HA-TBI and highlighting potential therapeutic targets for early intervention in high-altitude trauma.