Under dual pressures of energy scarcity and environmental pollution, the biobased polyester poly(ethylene furanoate) (PEF) is poised to dominate the industry in the future, overtaking conventional petroleum-based polyesters. Nonetheless, PEF discoloration is a critical impediment to its commercial success. Esterification reaction of 2,5-furandicarboxylic acid (FDCA) and ethylene glycol (EG) was developed at varying temperatures, yielding esterified products exhibiting varying degrees of discoloration. The main compounds and minor impurities in all esterified samples were accurately separated and identified using ultrahigh-performance liquid chromatography/ high-definition mass spectrometry (UPLC-HDMS) techniques. The chemical structure of the yellowing component was determined by secondary mass spectrometry (MS/MS), Fourier transform infrared (FTIR) spectrometry, and a nuclear magnetic resonance (NMR) spectrometer. It can be concluded that different forms of decarboxylated byproducts were produced during esterification and polycondensation, which resulted in the discoloration of PEF. At the same time, decarboxylated byproducts were also present in alcoholysis products of commercial brown PEF chips but absent in alcoholysis products of commercial white PET chips. These results clearly demonstrate a direct relationship between PEF discoloration and decarboxylation. Overall, this work offers theoretical support and insights for future research into PEF discoloration, establishing a solid foundation for further development and application.