Compared to the original Alpha variant, the novel coronavirus Omicron variant, as the main pathogen causing the global COVID-19 pandemic, exhibits stronger transmissibility. Although its pathogenicity has weakened, studies have shown that infection with the Omicron variant can still lead to neurological sequelae such as brain fog, taste and smell disorders, and headaches. To further investigate the molecular mechanisms of COVID-19 neurological sequelae such as brain fog and to advance drug target discovery, in this project, we conducted liquid chromatography-mass spectrometry (LC-MS) based proteomic and phosphoproteomic analyses on the frontal lobe, occipital lobe, parietal lobe, temporal lobe, cerebellum, and brainstem of rhesus monkeys infected with the SARS-CoV-2 Omicron variant. We found that the six brain regions showed specificity in their response to SARS-CoV-2 infection, but all exhibited immune responses. The differentially expressed proteins and predicted kinases identified in this study can serve as targets for screening candidate therapeutic drugs for COVID-19.