The tuberous roots of Ophiopogon japonicus and Liriope spicata are used for the same therapeutic purpose in traditional Chinese medicine and are collectively referred to as maidong medicine. Interestingly, it was observed that the price of tuberous roots varies depending on their location on the plant, and fibrous roots are usually discarded post-harvest. Mislabeling might be of concern due to similarities in morphological features between the two species. Moreover, paclobutrazol has been observed to be heavily applied during the production, and therefore might be of health concern. Overall, maidong might suffer from quality inconsistencies while its metabolomic complexity is influenced by growing region and cultivation practices, botanical species, and plant parts. To address these challenges, this study employed High-Performance Thin Layer Chromatography (HPTLC) approach, in which sample preparation and derivatization procedure were optimized to enable to capture more detailed and comprehensive metabolomic fingerprints. By integrating with rTLC algorithm and Multivariate Data Analysis (MVDA), an improved quality assessment was achieved. Samples were collected from four production regions and supplemented with commercial products from markets. The optimized HPTLC analysis recognized species- and region-specific metabolomic patterns of maidong, uncovering a 4% of mislabelled cases. Moreover, findings highlight the underexplored therapeutic potential of fibrous roots, and comparable therapeutic efficacy between different root types. Additionally, complemented by Liquid Chromatography-Mass Spectrometry (LC-MS) for paclobutrazol residue evaluation, 24.66% of the commercial maidong samples surpassed maximum residue limits of paclobutrazol, raising safety concerns. This research represents a significant analytical advancement, offering a robust, cost-effective, and comprehensive method for maidong quality control, and paving the way for more strict residue regulation and updates to herbal pharmacopoeias and monographs.