During autophagy, the intracellular components are captured in autophagosomes and delivered to lysosomes for degradation and recycling. Changes in lysosomal trafficking and contents are key events in the regulation of autophagy, which has been implicated in many physiological and pathological processes. In this work, two iridium(III) complexes (LysoIr1 and LysoIr2) are developed as theranostic agents to monitor autophagic lysosomes. These complexes display lysosome‐activated phosphorescence and can specifically label lysosomes with high photostability. Simultaneously, they can induce autophagy potently without initiating an apoptosis response. We demonstrate that LysoIr2 can effectively implement two functions, namely autophagy induction and lysosomal tracking, in the visualization of autophagosomal–lysosomal fusion. More importantly, they display strong two‐photon excited fluorescence (TPEF), which is favorable for live cell imaging and in vivo applications. Kill Two Birds with One Stone: Two iridium(III) complexes can specifically image lysosomes and induce an autophagic response in live cells. The combination of these two intriguing properties makes them ideal theranostic agents to track lysosomal changes during autophagic processes. Additionally, these complexes display strong two‐photon excited fluorescence, which is favorable for live cell imaging and in vivo applications.