Vanillin is naturally occurring in various food products, including alcoholic beverages; however, its contribution to the aroma of sake is unclear. In this study, an HPLC-MS/MS quantification method was developed and validated by linearity, precision, and recovery, and it was applied to 115 bottles of highly diversified sake. Furthermore, the odor detection threshold of vanillin in sake was determined. Notably, the established method exhibited great linearity (5–1500 μg/L), with a R2 >0.99, and the limit of detection and limit of quantification were 1.7 and 5.5 μg/L, respectively. The spiked recoveries of vanillin ranged from 96.2% to 97.8%, with relative standard deviation ˂ 6.22%. Results revealed trace amounts to 29.9 μg/L of vanillin in the premium young sake, below the detection threshold (78.9 μg/L), whereas aged sake (43 bottles, 3–56 years aging) exhibited varied concentrations from trace amounts to 1727.5 μg/L of vanillin, notably peaking in a 20-year oak barrel-aged sake. The concentration of vanillin in most of the ambient-temperature-aged sake exceeded the detection threshold after 11–15 years of aging. The proposed method facilitates accurate vanillin quantification in sake, crucial for evaluating its flavor impact. Moreover, the discoveries provide a theoretical basis for the sensory exploration of sake aromas and equip the brewing industry with insights for modulating vanillin synthesis during sake aging.