The photoinduced ligand desorption from nanocrystal (NC) surfaces plays a critical role in the diverse functionalities of NCs. However, this reaction is inherently complex because photophysical and photochemical reactions are involved, and many aspects remain elusive. In this study, using ZnS NCs coordinated with perylenebisimide (PBI) ligands as a model system, we revealed that pump-push-probe spectroscopy provides detailed insights into the transient species following photoinduced ligand desorption reactions. This method successfully isolated the signal of the PBI radical anion, generated by photoinduced charge separation, which was difficult to identify by conventional pump-probe spectroscopy. Furthermore, pump-push-probe spectroscopy also revealed that the transiently formed aggregation of PBI after PBI desorption is the H-type aggregate. This research is expected to contribute to the analysis of complex photochemical reaction processes in composite nanomaterials and is important for the development of highly efficient NC photocatalysts and photodurable NCs.