Phosphonate esters were synthesized and investigated by positive ion electrospray ionization mass spectrometry (ESI-MS) in conjunction with tandem mass spectrometry (MS/MS). It was found that for the sodiated adduct there were two novel rearrangement reactions, in which the phosphoryl oxygen atom migrated to the carbonyl carbon and a cleavage occurred at the amide bond, or a benzylamine fragment was lost and the phosphorus was reduced. However, when the methyl group substituted for the isopropyl group, these migrations were inhibited. A possible mechanism was proposed, and high-resolution mass spectrometry was applied to identify the formula of these novel ions. These results showed that ESI-MS is a useful tool for the structural determination of phosphonate esters.