The invention discloses a cement-based wave absorbing plate of a three-layer structure mixed with EP and an NGPs wave absorbing agent and a preparation method of the wave absorbing plate. The wave absorbing plate is composed of an upper layer plate, a middle layer plate and a lower layer plate according to a thickness ratio is 8:11:11. The upper layer plate comprises cement, silica fume, expandedperlite (EP) and a water reducing agent, wherein the silica fume, water, the expanded perlite and the water reducing agent account for 10%, 42%, 7% and 0. 32% of the mass of the cement respectively; the middle layer plate comprises the cement, the silica fume, the water, multi-layer graphene nanoplates (NGPs), nano-nickel particles and the water reducing agent, wherein the silica fume, the water,the multi-layer graphene nanoplates, the nano-nickel particles and the water reducing agent account for 10%, 32-33%, 0.025-0.05%, 0.7% and 0.33-0.35% of the mass of the cement respectively; the lowerlayer plate includes the cement, the silica fume, the water, carbon fibers, carbon black, the water reducing agent and a dispersing agent, wherein the silica fume, the water, the carbon fibers, the carbon black, the water reducing agent and the dispersing agent account for 10%, 74-80%, 0.5-1%, 4%, 0.35-0.36% and 0.35-0.38% of the mass of the cement. The wave absorbing plate is environmentally friendly and free of radioactivity, a preparation process is simple, and forming is convenient.