The decanting of red wines has a long tradition in red wine service from the perspective of modifying the aroma or taste of a wine. A simple and sensitive liquid chromatography-mass spectrometry method was developed for the simultaneous determination of 20 organic acids and polyphenols in decanting red wine. The separation was performed on a Diamonsil C18 column (250 mm × 4.6 mm, 5 μm) using a mobile phase composed of methanol-0.1% acetic acid under gradient elution. Analysis was performed in selected ion monitoring mode with negative electrospray ionization interface. All the linear regressions showed good linear relationships (r2 > 0.9973) between the peak area and concentration of each marker. The assay was reproducible with overall intra and interday variation of less than 5.0%. The recoveries for the quantified compounds were observed over the range of 92.1–108.3% with RSD values less than 5.7%. The method developed was successfully applied to determine the variations of the 20 components in red wine after decanting in different conditions. Concentrations of most organic acids and polyphenols investigated in the red wine were decreased in decanting. In addition, increment of duration, temperature, and light intensity would intensify the changes.