Currently, a preventive and curative treatment for COVID-19 is an urgent global issue. According to the fact that nanomaterial-based drug delivery systems as risk-free approaches for successful therapeutic strategies may led to immunization against COVID-19 pandemic, the delivery of Carmofur as a potential drug for the SARS-CoV-2 treatment via graphene oxide quantum dots (GOQDs) was investigated in silico using molecular dynamics (MD) simulation. MD simulation showed that π–π stacking together with hydrogen bonding played vital roles in the stability of the Carmofur–GOQD complex. Spontaneous attraction of GOQDs loaded with Carmofur toward the binding pocket of the main protease (M_pro) resulted in the penetration of Carmofur into the active catalytic region. It was found that the presence of GOQD as an effective carrier in the loading and delivery of Carmofur inhibitor affected the structural conformation of M_pro. Higher RMSF values of the key residues of the active site indicated their greater displacement to adopt Carmofur. These results suggested that the binding pocket of M_pro is not stable during the interaction with the Carmofur–GOQD complex. This study provided insights into the potential application of graphene oxide quantum dots as an effective Carmofur drug delivery system for the treatment of COVID-19.