The fast and nondestructive identification of mobile phone cases is a crucial task for law enforcement personnel in the field of forensic science. Attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) has been employed in conjunction with feature extraction and deep learning algorithms to develop a method for distinguishing mobile phone cases. As preprocessing steps, multivariate scatter correction and standard normal variate were performed. Feature variables were extracted using the competitive adaptive reweighted sampling and shuffled frog leaping algorithm. Several supervised pattern recognition methods, namely ResNet50, VGG16, and multilayer perceptron (MLP), were utilized for constructing classifiers. The results indicated that the model’s performance based on multivariate scattering correction (MSC) with competitive adaptive re-weighted sampling (CARS) surpassed that of other approaches. Notably, the ResNet50 model exhibited superior discriminative ability compared to the VGG16 and MLP models, achieving 100% accuracy in the differentiation of all samples. This designed method represents a potentially rapid and nondestructive approach for identifying mobile phone cases in forensic science.