The occurrence of the cooked off-flavor during the thermal sterilization of green tea beverages negatively impacts their quality. This study aimed to identify the key cooked off-flavor compounds by molecular sensory science. The increase of 12 compounds, including malty (e.g., 3-methylbutanal), floral (e.g., linalool), sweet (e.g., methional), and smoky (2-methoxy-4-vinylphenol) compounds, contributed to the development of the cooked off-flavor. Additionally, the loss of five aroma compounds—dimethyl sulfide, (E)-β-ionone, 2-methylbutanal, 1-penten-3-one, and (E,Z)-2,6-nonadienal—also caused the emergence this undesirable flavor. One potential solution to reduce the cooked off-flavor was the baking of tea raw materials. While baking did not significantly reduce the concentration of off-flavor compounds, it led to an increase in eight roasty aroma compounds, such as pyrazines and pyrroles, which helped partially mask the cooked off-flavor in green tea beverages.