Metal single-atom catalysts (M-SACs) have emerged as an attractive concept for promoting heterogeneous reactions, but the synthesis of high-loading M-SACs remains a challenge. Here, we report a multilayer stabilization strategy for constructing M-SACs in nitrogen-, sulfur- and fluorine-co-doped graphitized carbons (M = Fe, Co, Ru, Ir and Pt). Metal precursors are embedded into perfluorotetradecanoic acid multilayers and are further coated with polypyrrole prior to pyrolysis. Aggregation of the metals is thus efficiently inhibited to achieve M-SACs with a high metal loading (~16 wt%). Fe-SAC serves as an efficient oxygen reduction catalyst with half-wave potentials of 0.91 and 0.82 V (versus reversible hydrogen electrode) in alkaline and acid solutions, respectively. Moreover, as an air electrode in zinc-air batteries, Fe-SAC demonstrates a large peak power density of 247.7 mW cm-2 and superior long-term stability. Our versatile method paves an effective way to develop high-loading M-SACs for various applications.