Chili fermentation is one of the most important processes in the production of Pixian Douban (PXDB), which determines the flavor and product quality of PXDB. However, the maturity of fermented chili mainly depends on empirical judgment, which can not satisfy the need for standardized production of PXDB. Therefore, this study aimed to investigate volatile and non-volatile substances during the maturation process and to find markers related to the maturity of fermented chili. Two-dimensional gas chromatography-mass spectrometry (GC × GC-MS) combined with multivariate statistical analysis and relative odor activity values (ROAV) analysis revealed that 2-methoxy-3-isobutyl pyrazine, linalool, 3-(methylthio)propionaldehyde, myrcene, and decanal (ROAV ≥ 1, VIP > 1, P < 0.05) were regarded as potentially active aromatic markers for differentiating fermentation time. Additionally, ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) combined with multivariate statistical analysis revealed that 25 compounds could serve as differentiated non-volatile compounds. The correlation of maturity-related physicochemical indicators with volatile and non-volatile compounds revealed that four volatile compounds (2-methoxy-3-isobutylpyrazine, linalool, myrcene, and decanal) along with seven non-volatile compounds could serve as markers for evaluating the maturity of fermented chili. This study is expected to establish a standard for the determination of the maturity the fermented chili and lay the foundation for intelligent production of PXDB.