The identification of fructoborate complex in food matrices using liquid chromatography coupled with quadrupole Orbitrap mass spectrometry was investigated in this study. The LC/MS method was established by optimization of mobile phases and direct infusion of FruiteX-B^® brand calcium fructoborate (CaFB) solution to Q Exactive Orbitrap mass spectrometer to obtain MS operation parameters. The precursor ion m/z 367.10522 was dissociated further for conformation analysis of fructoborate complex. The method was applied to identify and quantify fructoborate in freeze dried apricot fruit and raisins. It was found that fructose-¹¹B-fructose di-ester complex was present in these fruits. The results were further verified by multinuclear solid and liquid states NMR spectroscopy analysis.