Lysosomes are crucial dynamic organelles which play key roles in different cellular processes such as autophagy, endocytosis and phagocytosis. Thus, long-term and real-time lysosomal imaging is desirable and essential to understand the dynamics and biological functions of lysosomes. Herein, ultra-stable carbon dots (CDs) which have shown many advantages such as pH-independence, high water solubility, good photostability and high biocompatibility for lysosome labeling and long-term tracking were synthesized using a one-pot pyrolysis method via microwave irradiation. Compared with the commercial lysosome probe (LysoTracker™ Deep Red), the fluorescent CDs show superior resistance to photobleaching and the HeLa cells were stably labeled by CDs for over 48 h. In addition, the CDs could stain lysosomes in different cell lines with high specificity and track lysosomal movements. Furthermore, the CDs could stain not only lysosomes in living cells, but also lysosomes in drug-induced apoptotic cells and fixed cells, suggesting that they are suitable for lysosomal tracking under both physiological and toxicological processes. All these excellent properties could be attributable to the ultrastability of CDs, which can be employed for constructing nanoplatforms for other applications such as drug carriers and signal guiders in biological processes. This study provides not only a strategy to synthesize green fluorescent CDs for tracking lysosomes, but also a promising candidate for drug loading and signal guidance of biological processes.