The intrinsic zero band gap structure and semi-metallic character of graphene has some limitations for applications in photonic devices. Therefore, its optical properties need to be tuned by functionalization followed by heteroatom doping and reducing the lateral dimensions up to a few nanometres. In this work, the fluorescence quantum yield of ‘as prepared’ graphene quantum dots (GQD) have been significantly improved by doping with the combination of heteroatoms (sulfur (S) and nitrogen (N)). The charge transfer interaction between these low dimensional systems and laser dyes is of significant importance in various fields. The feasibility of non-radiative resonance energy transfer between heteroatoms co-doped NS-GQD-dye systems has also been explored. The NS-GQD fluorescent nanoprobe has been found suitable to detect the H2O2 and, for deep-tissue imaging applications. In addition, the systems have also been probed with ultrafast laser pulses to understand the nonlinear optical responses for passive mode-locking applications.