Necrophagous flies and beetles represent the two most forensically significant insect taxa. The pupal stage of beetles typically exhibits a longer developmental duration and subtler morphological changes compared to flies. Therefore, accurately estimating the pupal age of necrophagous beetles is crucial for estimating the postmortem interval (PMI) during the decay and skeletonized stages of carcass decomposition, presenting a considerable challenge. This study first confirmed the above viewpoint by observing the pupal morphology of Dermestes ater DeGeer, 1774, a globally distributed dermestid species. Furthermore, the feasibility of characterizing the different pupal developmental times (pupal age) of necrophagous beetles was explored using attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy. The performance of seven machine learning regression algorithms–ANN, SVR, XGB-R, PLS-R, MLR, PCR, and CLR–was compared. The results revealed a gradual decrease in the intensity of absorption peaks corresponding to lipids and nucleic acids with increasing pupal age, while the amide I and amide II bands showed opposite trends, consistent with the biological processes of tissue dissociation and organ remodeling in pupal stage. The ANN model performed the best, with R2CV at 0.91, R2P at 0.91, and RMSECV at 0.88, indicating high estimation accuracy. SVR and XGB-R have also achieved satisfactory results. In conclusion, this study successfully applied FTIR spectroscopy combined with chemometrics for the first time to estimate the pupal age of beetles, offering an objective, rapid, reproducible, and cost-effective method. Future studies on the pupal stage of other necrophagous beetle taxa are needed to provide a comprehensive spectral database, aiding in long-term PMI estimation in forensic entomology.