Organic acids in honeys are currently quantified by enzymatic, capillary zone electrophoresis, and chromatographic methods; however, these methods have long analysis times and low sensitivities and selectivities. Here, we developed a simple, rapid liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based method for the determination of organic acids: gluconic acid, tartaric acid, malic acid, citric acid, and succinic acid in honey. First, we evaluated the linearity, matrix effects, detection limits, quantification limits, and repeatability of our method; the limit of detection for organic acids ranged from 0.005 to 0.70 mg/kg. In this study, it was 8 to 31 times higher sensitive than the high-performance liquid chromatography method. We then used our method to determine the concentrations of gluconic acid, tartaric acid, malic acid, citric acid, and succinic acid in 25 honey samples. Gluconic acid was found to account for 64.6 to 99.8% of the total organic acids in the samples. From the correlation and statistical analysis of each component, it is considered that the organic acid is produced by worker bee enzymes such as glucose oxidase and the TCA cycle. The developed method, which has high sensitivity and selectivity, will enable the analysis of more complex and low-concentration components.