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Red pepper (Capsicum annuum var. conoides) is commonly used for dried pepper production in China, and the drying process, particularly the during duration, profoundly affects its quality. The findings indicate that prolonged exposure to high temperatures during thermal drying results in significant darkening, an evident decrease in red and yellow tones, and gradual transformation of the pepper's microscopic structure from granular to compact, along with 88% reduction in moisture content and 81% decrease in thickness. The capsaicinoid content increased, resulting in a 4.3-fold increase in spiciness after drying compared to that of fresh pepper. The pepper aroma shifts from fruity, choking, and grassy to herb, dry wood, and smoky. Compounds such as 2-Acetylfuran, furfural, 2-methylfuran, 1-methylpyrrole, 2-methylpyrazine, and 2,5-dimethylpyrazine exhibited positive correlations with drying time, whereas ethyl 2-methylpropanoate, ethyl butanoate, ethyl 2-methylbutanoate, ethyl hexanoate, and 3-methylbutyl butanoate showed negative correlations, indicating their potential as markers for monitoring thermal drying processes.