The invention specifically discloses a graphene aggregate composite material, and a preparation method and application thereof, belonging to the field of graphene. The preparation method for the graphene aggregate composite material comprises the following steps: subjecting layered graphite, an oxidizing agent and an acid solution to an oxidation reaction so as to obtain graphite oxide; then subjecting the graphite oxide to high-temperature treatment to realize exfoliation of the graphite oxide into graphene so as to obtain graphene aggregate; and subjecting the graphene aggregate to high-temperature vapor deposition in the presence of gas capable of producing nanoparticles through high-temperature deposition so as to produce nanoparticles among different graphene layers of the graphene aggregate. According to the preparation method for the graphene aggregate composite material, the nanoparticles are deposited among the graphene layers, so lamellas are sufficiently isolated; and thus,a specific surface area is increased, and back lamination of graphene lamellas in later treatment can be prevented.