Biomass-based carbon quantum dots (CQDs) have become a significant carbon materials by their virtues of being cost-effective, easy to fabricate and low in environmental impact. However, there are few reports regarding using cyanobacteria as a carbon source for the synthesis of fluorescent CQDs. In this study, the low-cost biomass of cyanobacteria was used as the sole carbon source to synthesize water-soluble CQDs by a simple hydrothermal method. The synthesized CQDs were mono-dispersed with an average diameter of 2.48 nm and exhibited excitation-dependent emission performance with a quantum yield of 9.24%. Furthermore, the cyanobacteria-derived CQDs had almost no photobleaching under long-time UV irradiation, and exhibited high photostability in the solutions with a wide range of pH and salinity. Since no chemical reagent was involved in the synthesis of CQDs, the as-prepared CQDs were confirmed to have low cytotoxicity for PC12 cells even at a high concentration. Additionally, the CQDs could be efficiently taken up by cells to illuminate the whole cell and create a clear distinction between cytoplasm and nucleus. The combined advantages of green synthesis, cost-effectiveness and low cytotoxicity make synthesized CQDs a significant carbon source and broaden the application of cyanobacteria and provide an economical route to fabricate CQDs on a large scale.