Abstract: Objective: Cayenne pepper is a common variety used in the production of chili sauce abroad. However, it is rarely rarely studied and applied in China. Therefore, it is necessary to conduct the quality evaluation of fresh Cayenne pepper, and summary the quality characteristics of sauce using peppers. Methods: Targeted detection combined with non-targeted metabolomics technology was employed to conduct the quality evaluation on Cayenne pepper from Jiuquan City, Gansu Province and Bayannur City, Inner Mongolia Autonomous Region. More than 20 indicators such as moisture, sugar, acid, protein, capsaicinoids, carotenoids, volatile and non-volatile compounds were analyzed. Results: The moisture content of Cayenne pepper from Gansu and Inner Mongolia was 86.1% and 87.9%, the sugar content was 5.28 g/100 g and 4.67 g/100 g, the total acid content was 4.44 g/kg and 5.09 g/kg, and the spiciness level was 1386.26 SHU and 1116.41 SHU, respectively. Cayenne pepper from Gansu showed a higher sugar and capsaicinoids content, and a more abundant profile of volatile aromatic compounds, including methyl salicylate, ethyl 3-methylbutyrate, linalool and so on. On the other hand, Cayenne pepper from Inner Mongolia exhibited higher acid content and antioxidant capacity, and a more abundant profile of non-volatile compounds, including umbelliferone, quercetin, phytosphingosine and so on. Conclusion: Cayenne pepper, characterized by its high sugar content, mild spiciness, low seed-to-flesh ratio, and richness of aromatic and flavorful substances, meets the requirements for chili sauce processing. The peppers from different regions exhibit slight variations in quality, which make it necessary to evaluate the raw materials before sauce using species selection. This study will provide scientific guidance for the breeding and the selection of chili pepper varieties for sauce processing.