Mononuclear macrophages are important immune cells in the organisms. The complicated membrane structure underlying the diverse functions of mononuclear-macrophage has been largely unresolved. As a representative of monocyte-derived macrophages, the membrane structure of PMA differentiated THP-1 cells was comprehensively investigated by AFM-based single molecule approaches. The rugged ectoplasmic side of mononuclear-macrophage membrane are significantly different from erythrocytes and mammalian somatic cell membranes. But the smooth lipid bilayer and the branched lipid raft domains obtained by proteinase K and M beta CD treatment of the protein-covered cytoplasmic side, are common characteristics among all the studied cell membranes. This discovery of distinct organization of membrane proteins on both sides of mononuclear-macrophage membranes provides additional evidence for the asymmetry of membrane structure. The podosome-associated structures of mononuclear-macrophage were directly examined, and the independent localization of podosome domains and the lipid rafts was verified by in situ AFM, giving new insight into this multifunctional organelle.