According to the memory effect of layered double hydroxide (LDH), the LDH nanostructure containing polyoxometalates anion (LDH-MoP) was prepared by an anion exchange process. Compared with the original LDH contained carbonate ion (LDH-C), the LDH-MoP exhibited a hydrotalcite laminated structure with larger interlayer spacing than that of LDH-C, implying that the carbonate ions between LDH-C layers were replaced by polyoxometalates anions. The LDH-MoP obtained via replacement of anions by polyoxometalates anion could lead to a more homogeneous dispersion and better synergistic effect of flame-retardant components than those in the physically mixed sample of LDH-C and Na3[PMo12O40] ·xH2O. After adding 3 wt% LDH-MoP in epoxy resin (EP), EP/LDH-MoP shows the most significant decrease in peak heat release rate (PHRR), total heat release (THR), peak smoke rate (PSPR), and total smoke release (TSR). The Limited Oxygen Index (LOI) value of EP/LDH-MoP has been significantly improved, and a UL-94 V-0 rating (LOI = 32.1%) can be achieved. In addition, compared with that of the physical mixture, the EP/LDH-MoP generates a denser and more compact char residue after the cone calorimeter test, suggesting that the oxygen exchange, smoke diffusion, and heat transfer could be more effectively hindered during the combustion process of the latter. This study could provide a novel strategy for designing high-performance flame retardants and some valuable clues for the enhancement of homogeneous dispersion and the synergistic effect of inorganic flame retardants.