A highly sensitive, accurate, and selective LC–MS/MS method for the simultaneous quantification of polycarboxylic acids in fruits was developed by combining the derivatization of polycarboxylic acids, oxygen–heavy oxygen exchange reactions, and weak cation exchange solid-phase extraction. The derivatization reagent used in this method, namely TPP-AEP, effectively derivatizes polycarboxylic acids and enables highly sensitive LC–MS/MS analysis. Combined with the synthesis of internal standards by oxygen–heavy oxygen exchange reaction and selective SPE using a weak cation exchange column, 19 polycarboxylic acids could be accurately and selectively quantified. This method was applied to the quantitative analysis of polycarboxylic acids in fruits and 100% fruit juices from concentrated fruits, and the differences in their compositions were elucidated. The developed method exhibited good detection sensitivity, accuracy, and selectivity. These results are useful for preventing the counterfeiting of food products and improving the quality of fruit juice from the concentrate.