The important reason why aluminum hydroxide is widely used as a vaccine adjuvant is that it can be recognized and phagocytosed by antigen presenting cells (APC) such as dendritic cells (DC) and macrophages (M?). It can also enhance the immune response effectively by affecting the presentation ability of antigens. APC phagocytosis of antigens adjuvanted with aluminum adjuvant could activate lysosomes, mitochondria and other organelles, especially the mitochondria. A series of changes would occur in the mitochondria, including changes among reactive oxygen species (ROS), mitochondrial membrane potential (ΔΨm) and mitochondrial glycolipid metabolism, etc. Our research found that the antigens containing aluminum adjuvants can be rapidly phagocytized by macrophages and then an effective immune response can be induced. It is easy to find that the material basis of “fast phagocytosis and fast activation” should require more energy supporting. For this reason, we speculate that the biological behavior of mitochondria will be more active, and may cause “huge damage” to M? after the immune response is achieved. This review will give an overview of this phenomenon and elicit the thinking that needs to be solved in the next step.