Engineering of the luminescent properties for graphene quantum dots (GQDs) presents two enormous challenges: 1) The bandgap of GQDs is mainly determined by structural defects (size, shape, and the fraction of sp² and sp³ domains), which results in non-stoichiometric nature; 2) the preparation methods limit the achievement of an accurate chemical structure of GQDs, leading to many controversial explanations over the relationship between the structural defects and bandgaps. Here, single-layered GQDs with an exact structure are obtained by in-situ reaction of intercalated precursors in the confined nanospace of layered double hydroxides (LDHs). Subsequently, the structure-property relationship is uncovered, demonstrating the enhanced fluorescence and activated room temperature phosphorescence of the as-prepared GQDs-LDHs, which originate from synergistic effects: 1) strong confinement provided by the nanospace of LDHs; 2) rich O-containing functional groups on the surface of GQDs resulting from LDH catalysis. Moreover, the colorless nature and dual-emission characteristics of GQDs-LDHs satisfy the preconditions as anti-counterfeiting markers for protecting valuable documents (bank notes, commercial invoices, etc.). Particularly, owing to the low toxicity of GQDs and the edible property of LDHs, the GQDs-LDHs/gelatin capsules could be the new generation of potential green anti-counterfeiting material in the field of food and drugs.