A synergetic strategy was proposed to address the critical issue in the brand characterization of Colla corii asini (Ejiao, CCA), a precious traditional Chinese medicine (TCM). In all brands of CCA, Dong’e Ejiao (DEEJ) is an intangible cultural heritage resource. Seventy-eight CCA samples (including forty DEEJ samples and thirty-eight samples from other different manufacturers) were detected by laser-induced breakdown spectroscopy (LIBS) and near-infrared spectroscopy (NIR). Partial least squares discriminant analysis (PLS-DA) models were built first considering individual techniques separately, and then fusing LIBS and NIR data at low-level. The statistical parameters including classification accuracy, sensitivity, and specificity were calculated to evaluate the PLS-DA model performance. The results demonstrated that two individual techniques show good classification performance, especially the NIR. The PLS-DA model with single NIR spectra pretreated by the multiplicative scatter correction (MSC) method was preferred as excellent discrimination. Though individual spectroscopic data obtained good classification performance. A data fusion strategy was also attempted to merge atomic and molecular information of CCA. Compared to a single data block, data fusion models with SNV and MSC pretreatment exhibited good predictive power with no misclassification. This study may provide a novel perspective to employ a comprehensive analytical approach to brand discrimination of CCA. The synergetic strategy based on LIBS together with NIR offers atomic and molecular information of CCA, which could be exemplary for future research on the rapid discrimination of TCM.