Fermented Fructus Aurantii (FFA) is widely used in South China for the treatment of functional dyspepsia. Naringin, neohesperidin, and other flavonoids are the main pharmacodynamic components of FFA. A new method is presented for the simultaneous determination of 10 flavonoids (including flavonoid glycosides and aglycones) in FFA using the quantitative analysis of multicomponents via a single marker (QAMS) approach and is used to investigate changes in flavonoids during fermentation. The viability and precision of QAMS were validated against the ultrahigh-performance liquid chromatography (UPLC), with various UPLC instruments and chromatographic conditions being evaluated. Differences between raw Fructus Aurantii (RFA) and FFA were examined using orthogonal partial least squares discrimination analysis (OPLS-DA) and content determination. The influence of various fermentation conditions on flavonoids was also investigated. There were no appreciable differences between the QAMS and the external standard method (ESM), demonstrating that QAMS is an improved method for the determination of FA and FFA. FFA and RFA can be readily distinguished based on OPLS-DA chemometric modelling and the corresponding chromatograms. In addition, the flavonoid changes after fermentation. Fermentation considerably reduced the contents of flavonoid glycosides, while increasing hesperidin-7-O-glucoside and flavonoid aglycones. Moreover, fermentation conditions impact multiple flavonoids in FA, so controlling these conditions is necessary for the quality control of fermented FA products. This QAMS approach is useful for detecting numerous components in RFA and FFA simply, quickly, and efficiently, thus strengthening the quality control of FA and its fermented products.