Although chemotherapy remains a prevalent option in cancer treatment, its adverse effects on normal cells and suboptimal pharmacokinetics often limits its effectiveness. To address these challenges, this study successfully developed a new multifunctional drug delivery system comprising a covalent composite of graphene quantum dots and barium titanate nanoparticles. Notably, despite numerous reports on the surface modification of graphene quantum dots, studies focusing on cancer cell inhibition via different covalent bonds are scarce. To bridge this gap, this system was synthesized using eco-friendly esterification and amidation pathways. The anticancer drug doxorubicin was employed as a model drug, and hyaluronic acid was used to encapsulate the delivery system, enhancing its sustained release capabilities. Comprehensive material characterization confirmed the successful synthesis of the system. Its high drug loading capacity and acid-sensitive release can be attributed to the unique structure of the graphene quantum dots. Subsequent in vitro and in vivo biological evaluations not only demonstrated the system’s remarkable cancer inhibition efficacy but also accentuated the distinct impacts of the two bonding types. The underlying mechanism is believed to involve bonding affinity and electron transfer, findings that are corroborated by the experimental data. Additionally, results from animal models provide clear evidence for the potential application of this system (HA-DOX-GQD@BTNPs) in cancer therapeutics and imaging. In conclusion, this research elucidates the variances in drug carrier efficacy based on different covalent bond modifications for cancer treatment and introduces a novel drug delivery system that synergistically combines imaging and targeting capabilities.