Background: Methanol is a toxic alcohol for the human body. The molecular biology of methanol metabolites affecting different organs, such as the brain, is under investigation. This systematic review aimed to consider methanol toxic molecular biology, based on the original articles obtained from data banks to figure out recent achievements. Methods: Scientific articles regarding the toxic effects and metabolites of methanol on the central nervous system (CNS) were collected from valid databases and classified based on their validity. Exclusion criteria were articles with duplicates, no available full text, review articles, case reports, and letters. Results: Current metabolic reactions were addressed in the development of CNS diseases, such as optic neuropathy, basal ganglia lesions, and Alzheimer’s disease. However, proteomic investigations introduced new metabolic changes, and serum proteins regarding blood coagulation, vitamin A metabolism, and immune responses were suggested for early detection of toxicity. Conclusion: Besides CNS disorders introduced for methanol toxicity, there is no exact proteomic serum marker to diagnose toxicity soon; however, the interleukin-1 beta system is suggested as a candidate, and more investigation is required to improve its competency.