We fabricate transparent cellulose nanopapers with significantly enhanced flame retardancy by a vacuum filtration assisted layer-by-layer deposition method. Flame retardancy is enhanced by increasing the layer-by-layer thickness while not hampering optical transparency of the nanopapers. Thermal degradation and combustion behaviors show that the nanopapers have been successfully functionalized by phosphorus and amine compounds that act effectively as intumescent and blowing agents. Based on the heat release rate of the various nanopapers herein, we propose that the area of the second peak in the heat release rate can serve as an indicator for coating efficiency of these flame retardant materials. We also suggest a possible mechanism behind the material’s flame retardancy where by the phosphorus and blowing materials promote intumescent carbonaceous and porous char layers that prevent diffusion of oxygen and heat penetration into the underlying cellulose nanopapers.