The invention discloses a high damping concrete based on internal structure design and a preparation method thereof. The high damping concrete comprises a common concrete restraining layer and polymer modified layers. One or two polymer modified layers are introduced into the common concrete restraining layer so as to form the multiple restraining layer-free layer-restraining layer vibration attenuation unit combination; the common concrete restraining layer comprises 15-17 parts of cement, 30-35 parts of natural river sand, 42-47 parts of macadam, 4-8 parts of water and 1-2 parts of a water reducing agent; each polymer modified layer comprises polymer emulsion or polymer modified mortar. The high damping concrete disclosed by the invention has excellent absorbing and energy-dissipating functions and has excellent vibration attenuation and noise-absorbing properties, and meanwhile, the mechanical properties, such as fracture resistance and compressive strength, are controlled within reasonable scope.