Graphene quantum dots (GQDs) have recently emerged as a promising type of low-toxicity, high-biocompatibility, and chemically inert fluorescence probe with a high resistance to photobleaching. They are a prospective substitution for organic materials in light-emitting devices (LED), enabling the predicted concept of much brighter and more robust carbon LED (CLED). However, the mechanism of GQD emission remains an open problem despite extensive studies conducted so far, which is becoming the greatest obstacle in the route of technical improvement of GQD quantum efficiency. This problem is solved by the combined usage of femtosecond transient absorption spectroscopy and femtosecond time-resolved fluorescence dynamics measured by a fluorescence upconversion technique, as well as a nanosecond time-correlated single-photon counting technique. A fluorescence emission-associated dark intrinsic state due to the quantum confinement of in-plane functional groups is found in green-fluorescence graphene quantum dots by the ultrafast dynamics study, and the two characteristic fluorescence peaks that appear in all samples are attributed to independent molecule-like states. This finding establishes the correlation between the quantum confinement effect and molecule-like emission in the unique green-fluorescence graphene quantum dots, and may lead to innovative technologies of GQD fluorescence enhancement, as well as its broad industrial application.