This study systematically investigated four types of graphene quantum dots (GQDs) AHEX, ZTRI, ZHEX, and ATRI, and their interactions with glycine to form GQD-glycine complexes. Utilizing density functional theory (DFT) and the PM6 semiempirical method, the study analyzed electronic properties and structure-activity relationships. Global reactivity indices were calculated using Koopmans’ theorem, and quantitative structure-activity relationship (QSAR) parameters were assessed via SCIGRESS 0.3. The study further explored interactions using density of states (DOS) and quantum theory of atoms in molecules (QTAIM) analyses. Key findings revealed that glycine interaction significantly increased the total dipole moment (TDM) and decreased the HOMO/LUMO energy gap (ΔE) for the GQD-glycine complexes. Notably, ZTRI/glycine showed a TDM of 4.535 Debye and a reduced ΔE of 0.323 eV, indicating enhanced reactivity. Further interactions with cellulose, chitosan, and sodium alginate identified the ZTRI/glycine/sodium alginate composite as the most reactive, with a TDM of 8.020 Debye and the lowest ΔE of 0.200 eV. This composite also exhibited the highest electrophilicity index (56.421) and lowest chemical hardness (0.145 eV), underscoring its superior reactivity and stability. DOS analysis revealed that biomolecules contributed the most to molecular orbitals, with carbon atoms contributing the least. QTAIM analysis confirmed the greater stability of the ZTRI/glycine/sodium alginate complex compared to other studied composites. These results highlight the enhanced reactivity and stability of GQDs when interacting with glycine and sodium alginate.