Ginger flavor beverages (GFBs) were sterilized using different methods including ultra-high-temperature sterilization (UHT) (135 °C, 5 s), atmospheric pressure sterilization (AP) (95 °C, 30 min), and high-pressure sterilization (HP) (121 °C, 15 min). Comparative study of flavor among beverages from different sterilization methods was performed using quantitative descriptive sensory analysis and electronic nose (EN) and gas chromatography–mass spectrometry (GC–MS). Seven attributes (fruity, floral, gingery, piquant, sweet, sour, and cooked) were selected to assess ginger beverage flavors. The odor profile features of GBFs from different sterilization methods were determined by EN, and fifty-nine volatile compounds were detected by GC–MS. Partial least squares regression (PLSR) was performed to analyze the correlation among data of quantitative descriptive sensory analysis, GC–MS data, and EN responses of GFBs. The results showed that nine volatile compounds, (E,E)-α-farnesene, eucalyptol, l-linalool, borneol, citronellol, β-bisabolol, geranial, bornyl acetate, and neryl acetate, had significant positive contribution to gingery note, and further, PLSR showed that AP was the most beneficial method to preserve these important volatile compounds. Conclusively, AP was chosen as the most favorable method for sterilization of clarified GFBs.