Phototherapeutic diagnostics has attracted ever increasing interest due to its substantial promise within conventional cancer therapeutic paradigms. Consequently, the development of multi-functional phototherapeutic agents targeting specific organelles to uncover the close association of specific organelles with apoptotic signaling pathways is particularly appealing yet difficult to achieve. Here, we propose the concept of a crosstalk-free multi-functional phototherapeutic agent. This innovative phototherapeutic agent enables the concurrent delivery of highly efficient phototherapeutic treatment and crosstalk-free imaging, employing a dual-channel strategy. Differing from predecessors with single-channel multi-functional phototherapeutic functions, we engineered a dual-channel system to mitigate the competition between non-radiative and radiative relaxation processes, enabling both high fluorescence quantum yield and high photothermal conversion efficacy in one multi-functional phototherapeutic agent. The theranostic agent NIR-Cz was designed using this concept. Last but not least, using NIR-Cz, at a cellular level and in vivo, we observed a correlation between the average quantity of lipid droplets and the degree of apoptosis, which exhibited an increase with a non-monotonic trend and variable fluctuations. The concept of crosstalk-free multi-functional phototherapeutic agents is expected to provide a suite of powerful tools to elucidate the intricate relationships between organelles and apoptotic signaling pathways.