Fermented chopped chili pepper (FCCP) is the most important fermented and processed chili pepper product, and most pepper varieties can be processed with obvious flavor differences. Many studies have tried to explain these differences using the results of component analysis, processing technology, the microbes involved, etc., but few have examined the characteristics of these varieties along with the flavor of products. We conducted a physiochemical characteristic analysis of 35 kinds of fresh chili peppers with different genotypes and made fermented products from 17 varieties, using principal component analysis (PCA) and cluster analysis (CA) to correlate their components with FCCP products. The results were as follows: (1) Protein, total acids, a* (representation of the object’s red and green color), protopectin, and fruit thickness are the five key indexes that affect the quality of fresh chili peppers the most. (2) Protein, total acids, a*, protopectin, and fruit thickness are also the key indexes that affect the quality of FCCP. (3) Suitable ranges of fresh chili pepper to manufacture FCCP are 1.3–2.0 g/100 g for protein, 2.5–4.0 g/kg for total acids, 10–15 g/100 g for protopectin, 30–39 for a*, and 1.2–2.0 mm for fruit thickness. (4) Sensory appraisal shows crispness is the most important mouthfeel sensation and can decrease during the process. The varieties with the top three scores were A12 (21G675), A13 (20Z663), and A14 (21Z698) with scores of 87.92, 74.08, and 74.15, respectively. The varieties in the top three scores are pod peppers. The PCA and CA showed that pod peppers were the most suitable materials for making FCCP. Our results will benefit others in selecting fresh chili peppers for making FCCP and provide data support for directing processable variety breeding.