The invention provides a method for directly preparing graphene quantum dot arrays on an insulation substrate. The preparation method comprises the following steps: a GOI structure is provided, and comprises the insulation substrate and a germanium layer formed on the insulation substrate; the GOI structure is annealed to form germanium quantum dot arrays on the insulation substrate; the graphenequantum dot arrays are formed on the germanium quantum dot arrays; all graphene quantum dots in the graphene quantum dot arrays correspond to all germanium quantum dots in the germanium quantum dot arrays; the germanium quantum dots are wrapped by the graphene quantum dots; and the germanium quantum dot arrays in the structure obtained in the previous steps are oxidized and volatilized to remove the germanium quantum dot arrays so as to realize direct preparation of the graphene quantum dot arrays on the insulation substrate. The method solves the problem of incapability of preparing the graphene quantum dot arrays arranged in sequence in the prior art.