Protein modification by methylation is one of the main ways of protein post-translational modification. More and more reports have confirmed the existence of protein methylation in archaea. Methyltransferases that are involved in the post-translational modification in archaea have been identified but their mechanism is still unclear. This article summarizes the methyltransferases reported so far and the possible roles of protein methylation. Protein methylation in archaea can improve the protein stability, affect side chain conformational changes, and facilitate interaction with other molecules. The modified proteins include those in DNA damage repair and stress response. Finally, future research directions of archaeal protein methylation are proposed.