The thermal alteration of chlorophyll-a (Chl-a) was examined by means of thermogravimetry (TG) and pyrolysis—gas chromatography (Py-GC). Py-GC/mass spectroscopy, gas chromatography and infrared spectrometry were also used as complementary methods. When pyrolyzed at 340 °C for 15 s, Chl-a produced virtually only C20-isoprenoid hydrocarbons (C20-ISOPs). This result indicates that the major decomposition reaction below 340 °C is the release of a phytyl (3,7,11,15-tetramethyl-2-hexadecenyl) chain. When the 340 °C-pyrolysis residue was pyrolyzed again at 470 °C for 15 s, notable amounts of isoprenoid hydrocarbons with carbon numbers of 19 or less (S-ISOPs) were produced and amounts of C20-ISOPs became smaller. We assume that these S-ISOPs are produced from a phytanylaromatic structure which may have been formed during the 340 °C pyrolysis. On heating Chl-a at 150 °C for a long time (504 h) resulted in the formation of a material barely soluble in many organic solvents. S-ISOPs produced from the barely soluble material upon pyrolysis at 470 °C are similar in molecular distribution to those obtained by the pyrolysis at 470 °C of the 340 °C-pyrolysis residue of Chl-a. This suggests that a phytanyl-aromatic structure is formed also on long-term 150 °C heating. The Chl-a-derived S-ISOPs were almost identical to those obtained upon flash pyrolysis of kerogens (insoluble organic matter in sedimentary rocks) in terms of molecular composition. Thus, it is supposed that Chl-a changes into a polycondensed material having a phytanyl-aromatic structure in sediments/sedimentary rocks and is finally incorporated into a kerogen assemblage in nature.