Chemical functionalization and heteroatom doping are two effective strategies for improving the conductivity of a graphene lattice. Nitrogen-doped graphene oxide quantum dot (GOQD) has been reported to possess both p- and n-conductivity that is induced by an oxygen functional group and nitrogen doping, respectively, and is suitable for catalyzing hydrogen and oxygen evolution reactions for complete water splitting. The experimental study shows that the hydrogen evolution reaction occurs considerably faster than the oxygen evolution reaction. However, the mechanism of this phenomenon remains unknown, which poses a challenge to the chemical modification of such classes of materials. In the present work, we perform nonadiabatic ab initio molecular dynamics to explore the charge separation dynamics in N-doped GOQD with oxygen functional groups. Our results show that there exists multiple charge decay channels governed by different mechanisms, which complicates the overall charge separation dynamics in N-doped GOQD. The intramolecular electron transfer mainly occurs through the nonadiabatic channel, whereas the intramolecular hole transfer mainly occurs through the adiabatic channel. There is an additional adiabatic decay channel in the p-domain, which accelerates electron–hole recombination in the p-domain. We further calculated the decoherence times and found that the decoherence of intramolecular electron transfer occurs considerably faster than that of hole transfer, which slows the quantum transition of intramolecular electron transfer. Finally, we simulated the carrier relaxation times and found that the electron relaxation is approximately one order of magnitude longer than that of the hole relaxation. Our calculation rationalizes the experimentally observed higher catalytic activity towards the hydrogen evolution compared to the oxygen evolution. More importantly, the calculation explains the fundamental roles of nitrogen doping and oxygen functional groups in the adiabatic and nonadiabatic charge decay mechanisms.