The temporal and spatial distribution differences in the main flavor compounds in the fermented grains of strong aroma baijiu from central Sichuan were analyzed by gas chromatography-mass spectrometry. The results showed that there were 132 flavor compounds in the marginal fermented grains, including 44 esters, 26 alcohols, and 14 acids. In total, 127 flavor compounds, including 58 esters, 27 alcohols, and 15 acids, were identified in the main fermented grains. Acetic acid, butyric acid, caproic acid, ethyl lactate, ethyl caproate, ethyl linoleic acid, and ethyl hexadecanoic acid were the different metabolites produced during the fermentation process. In the marginal fermented grains, levels of caproic acid and butyric acid gradually increased initially, and thereafter rapidly increased in the middle to late stages. The ethyl hexadecanoate and ethyl linoleate contents in the main fermented grains reached their respective peak values (23.14 and 12.90 μg/g) in 76 days. The aim of this research was to establish a theoretical foundation for solid-state brewing and stabilize the quality of strong aroma baijiu in the central Sichuan region.