Here, two dimensional Nb2C quantum dots with green fluorescence were fabricated for the first time with a quantum yield (QY) of up to 19%, the highest reported for Nb2C dots so far with good photostability and pH stability. The S,N doping on Nb2C was considered to be the main reason for the enhanced high QY of the Nb2C dots and was proved by the density functional theory (DFT) calculations. It was demonstrated that the fluorescent probe could be utilized effectively for 3D brain organoid labeling and thus has huge prospects in biological sensing.