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The effects of (fresh/aged) brine and (pool/jar) containers on the flavor characteristics of pickled chili peppers were investigated based on a multivariate analysis integrated with kinetics modeling. The results showed that the effect of brine on organic acid, sugar, and aroma was more dominant than that of containers, while free amino acids production was more affected by containers than brines. Chili pepper fermented using aged brine exhibited higher acidity (3.71–3.92) and sugar (7.92–8.51 mg/g) than that using fresh brine (respective 3.79–3.96; 6.50–9.25 mg/g). Besides, chili peppers fermented using pool containers showed higher free amino acids content (424.74–478.82 mg/100 g) than using a jar (128.77–242.90 mg/100 g), particularly with aged brine. As for aroma, the number of volatiles in aged brine was higher (88–96) than that in fresh brine (76–80). The contents of the esters, alcohols, and ketones were significantly higher in the aged brine samples than those in fresh brine (p < 0.05), while terpenes in chili pepper fermented using the pool were higher than those using the jar. In general, jar fermentation with aged brine contributed more flavor to pickled chili peppers than other procedures.