Graphene quantum dots (GQDs) and carbon nitride quantum dots (CNQDs), the latest addition to the carbon material family, are promising materials for numerous novel applications in optical sensing, photocatalysis, biosensing, and photovoltaics. However, understanding the photocatalytic capability of CNQDs compared to GQDs requires investigations of the charge behavior on the excited state energy surface. In this work, through time-dependent density functional tight binding (TD-DFTB) calculations, we show that CNQDs exhibit superior ground state frontier orbitals (FOs) localization. Strong localization of the FOs and excited state charge separation observed in the first excited state are caused by the relaxation of the structure. Excited energy surface investigations reveal spatial confinement of FOs to the stretched C-N bonds due to excited state structural relaxation. On the other hand, no such localized FOs structure was found for GQDs, presumably caused by its strong π-conjugated configuration not allowing large structural changes upon excitation. The optical absorption and emission of CNQDs is sensitive to size and does not show large variations with the shape of the QD. Our approach provides an explanation for the origin of the enhanced photocatalytic performance of CNQDs over GQDs and their characteristic FOs localization.