A method for the determination of nine biogenic amines (BAs) in wine was established using ion chromatography–tandem mass spectrometry (IC-MS/MS) without derivatization. BAs were separated by a cation exchange column (IonPac CG17, 50 mm × 4 mm, 7 µm) with a gradient aqueous formic acid elution. Good linearity was obtained for nine BAs with coefficients of determination (R2) > 0.9972 within the range of 0.01–50 mg/L. The limits of detection and quantification were within the ranges of 0.6–40 µg/L and 2.0–135 µg/L, respectively, with the exception of spermine (SPM). The recoveries were demonstrated within the range of 82.6–103.0%, with relative standard deviations (RSDs) of less than 4.2%. This simple method featuring excellent sensitivity and selectivity was suitable for the quantification of BAs in wines. The occurrence of BAs in 236 wine samples that are commercially available in China was determined. The BA levels in wines of different geographical origins varied significantly. The acute dietary exposure assessment of BAs was carried out by calculating the estimated short-term intake (ESTI) and comparing the acute reference dose (ARfD) specified by the European Food Safety Authority (EFSA). Results showed that the exposure to histamine (HIS) and tyramine (TYR) via the consumption of wines was much lower than the recommended ARfD level for healthy individuals. However, exposure could lead to symptoms in susceptible individuals. These results provided basic data regarding the occurrence and risk of BAs in wines for wine production, health guidance and consumer safety.