Disclosed are an embedded co-cured composite material with large-damping and electromagnetic wave absorbing properties and a preparation method and an application thereof, belonging to damping composite materials. The embedded co-cured composite material is formed by interlacing a plurality of electromagnetic wave absorbing prepreg layers and a plurality of electromagnetic wave absorbing damping layers. Each of the electromagnetic wave absorbing prepregs layers includes a fiber cloth, a micro-nano electromagnetic wave absorbing material and a resin. Contents of the micro-nano electromagnetic wave absorbing material in the electromagnetic wave absorbing prepreg layers and the electromagnetic wave absorbing damping layers have a gradient increase or decrease according to a sequence of the electromagnetic wave absorbing prepreg layers. Each of the electromagnetic wave absorbing damping layers includes a viscoelastic damping material and the micro-nano electromagnetic wave absorbing material.