In this study, aroma profiles of fresh and fermented chili pepper from nine Capsicum frutescens cultivars were compared using untargeted analysis based on headspace solid phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS). Furthermore, multivariate data analysis was adopted to identify the characteristic aroma compounds of fermented chili pepper. The results showed that esters and terpenes were the major characteristic volatile components in fresh chili pepper. The number and amount of esters and terpenes increased significantly after fermentation (P < 0.05). Ocimene, hexanal, (E)-2-hexanal, 1-hexanol, linalool, methyl salicylate, and 4-methylpentyl 3-methylbutanoate were common to fresh chili pepper from the nine cultivars, while the volatile aroma compounds common to fermented chili pepper were (E)-2-heptanal, (E)-2-octenal, 1-octene-3-one, (E)-linalool oxide (furanoid), ethyl salicylate and α-terpineol. 1-Octene-3-one and (Z)-3-hexenyl hexanoate were the most predominant aroma-active compounds in fresh and fermented chili pepper, respectively. Moreover, a significant difference was observed among cultivars in terms of the profile of aroma compounds. The multivariate data analysis indicated that esters (benzyl 2-methylbutanoate, pentyl 3-methylbutanoate, benzyl pentanoate) and terpenes (D-limonene, ocimene, anethole) contributed to the difference in the flavor of fermented chili pepper among cultivars. The aroma profile of fermented chili pepper described in this study can provide theoretical support for flavor evaluation of and variety selection for fermented chili pepper.