The reaction of diols with isocyanates, leading to mono-functional and di-functional prepolymers may be investigated using various characterization methods which show the overall conversion of isocyanate monomers. On the other hand, matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) polymer characterization can be employed to identify the monomer units, the end-group functionalities, molecular weight averages, and to determine the copolymer sequence. Herein, we focus on prepolymer synthesis using isophorone diisocyanate (IPDI), a widely used diisocyanate for prepolymers preparation, especially in waterborne polyurethane materials. Thus, the reaction between polyethylene glycol diol and IPDI was in-depth investigated by mass spectrometry to determine the influence of the reaction parameters on the prepolymer’s structure. The relative content of the different functional oligomer species at given reaction times was determined in the reaction mixture. More specifically, the offline analysis revealed the influence of reaction parameters such as reaction temperature, the concentration of reactants, and the amount of dibutyltin dilaurate catalyst. The established MALDI MS analysis involved measurements of samples, first, directly collected from the reaction mixture and secondly, following derivatization with methanol. The obtained results revealed the effects of reaction parameters on the functionalization reaction with isocyanates, allowing to achieve a better reaction control.