Substituted ureas correspond to a class of organic compounds commonly used in agricultural and chemical fields. However, distinguishing between different ureas and differentiating substituted ureas from other compounds with similar structures, such as amides, N-oxides, and carbamates, are challenging. In this paper, a four-stage tandem mass spectrometry method (MS4) is introduced for this purpose. This method is based on gas-phase ion-molecule reactions of isolated, protonated analytes ([M + H]+) with tris(dimethylamino)borane (TDMAB) (MS2) followed by subjecting a diagnostic product ion to two steps of collision-activated dissociation (CAD) (MS3 and MS4). All the analyte ions reacted with TDMAB to form a product ion [M + H + TDMAB - HN(CH3)2]+. The product ion formed for substituted ureas and amides eliminated another HN(CH3)2 molecule upon CAD to generate a fragment ion [M + H + TDMAB - 2HN(CH3)2]+, which was not observed for many other analytes, such as N-oxides, sulfoxides, and pyridines (studied previously). When the [M + H + TDMAB - 2HN(CH3)2]+ fragment ion was subjected to CAD, different fragment ions were generated for ureas, amides, and carbamates. Fragment ions diagnostic for the ureas were formed via elimination of R-N═C═O (R = hydrogen atom or a substituent), which enabled the differentiation of ureas from amides and carbamates. Furthermore, these fragment ions can be utilized to classify differently substituted ureas. Quantum chemical calculations were employed to explore the mechanisms of the reactions. The limit of detection for the diagnostic ion-molecule reaction product ion in HPLC/MS2 experiments was found to range from 20 to 100 nM.