Kiwifruit puree was treated with high and normal temperatures and pressures as independent variables to determinate the structural changes of chlorophyll derivatives. Two groups of colored elution samples were identified as single component compounds by High Performance Liquid Chromatography (HPLC). In addition, the structures of the two compounds were identified and analyzed by High Resolution Mass Spectrometry (HRMS) and Nuclear Magnetic Resonance (NMR). The results of HRMS and NMR demonstrate that components 1 and 2 were hydroxymethylbilane (HMB) and red chlorophyll catabolite (RCC), respectively, and indicate that HMB and RCC were the main pigments in the chlorophyll compounds after high temperature and pressure treatment. Furthermore, the cleavage pathway of the RCC in kiwifruit puree has been discussed, which provides a theoretical basis for the color protection of kiwifruit products in the course of processing.