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In Jeju-native <i>Citrus</i>, flavonoids are the main contributors to the various types of biological activity, such as antioxidant, antitumor, and anti-inflammatory activity. Thus, we developed simultaneous quantification methods for the analysis of ten bioactive flavonoids in Jeju <i>Citrus</i> fruits (Dangyuja, Gamja, Jigak, Sadugam, and Soyuja) harvested at six different time points using a high-performance liquid chromatography–diode array detector (HPLC-DAD). Separation was performed using a flow rate of 0.8 mL/min, a column temperature of 40 °C, a mobile phase buffer of 0.5% acetic acid, and a detection wavelength of 278 nm. The established analytical method showed good linearity (R² ≥ 0.9997), precision (inter-day < 0.599%, intra-day < 0.055%), and accuracy (recoveries 92.30–108.80%). The HPLC–DAD method was subsequently applied to analyze flavonoids in <i>Citrus</i> samples. Overall, the quantification results indicated that the compositions and content of flavonoids differed for each <i>Citrus</i> species. The harvesting period also influenced the changes in flavonoid content within each <i>Citrus</i> species. The analytical results with chemometrics revealed that higher flavonoid levels in early-harvested <i>Citrus</i> were derived from the improved fruit size and reduced flavonoid synthesis during maturation. This study provides a practical and reliable method for the analysis of ten flavonoids that can be further utilized in the quality assessment of Jeju <i>Citrus</i>.