Abstract: The heterogeneous cracking process of ultra-deep oil is well-studied, yet the geochemical evolution mechanisms of crude oil pyrolysis at the microscale remain unclear. This study conducts a closed-system gold-tube thermal simulation experiment on low-maturity crude oil to obtain pyrolysis residual oils and soluble asphaltenes at different thermal evolution stages. It also introduces the first application of optical photothermal infrared spectroscopy (O-PTIR) at submicron scales to analyze the molecular composition and functional group heterogeneity of residual organics during crude oil pyrolysis. The results indicate that in the early rapid pyrolysis phase, biomarkers in crude oil maintain source characteristics consistent with the original oil. By the end of this phase, aliphatic compounds are fully pyrolyzed, while aromatic biomarkers continue to effectively reflect the high-temperature thermal evolution degree of the crude oil. The two light oil samples exhibited similar molecular structural evolution patterns. At EasyRo = 1.33%, O-PTIR spectra display a marked absorption band near 1720 cm−1, with CH3 and CH2 maps showing strong infrared signals, revealing patchy and striped contours of residual asphaltene particles. Pseudo-van Krevelen analysis indicated the gradual generation or growth of short-chain hydrocarbons during the thermal cracking process. At EasyRo = 1.81%, the aromatization degree of compounds increased, with distinct peaks for CH3, CH2, C=C, and C=O functional groups. The 2D synchronous IR spectra showed a strong correlation between autocorrelation peaks and point spectra, with no regional enrichment, indicating a significant reduction in molecular structural heterogeneity. Furthermore, the overall trends in the 2D IR spectra of the asphaltenes were similar, with noticeable autocorrelation and positive cross peaks at 1600 and 1720 cm−1, indicating that the spectral intensity increased or decreased synchronously during thermal evolution. This study reveals, at the molecular scale, the evolution of organic compounds and functional groups during crude oil cracking and offers valuable insights for expanding O-PTIR applications in petroleum geology.