Hylomecon japonica (Thunb.) Prantl et Kundig (Hylomecon japonica) is a perennial medicinal herb of the family Papaveraceae whose rhizomes are widely used in traditional medicine. Fresh rhizomes are prone to rapid browning after harvest, which affects their appearance and may compromise the stability of their bioactive components; however, the enzymatic basis of this browning and the effects of drying methods on quality-related components remain largely unclear. In this study, polyphenol oxidase (PPO) and peroxidase (POD) activities were determined under different low-temperature treatments to investigate their potential roles in the enzymatic basis of browning, and the effects of eight drying methods—shade drying (SD), oven drying at 60 °C (OD-60), vacuum drying at 40 °C (VD-40), boiling followed by freezing and freeze-drying (BF-FD), direct freeze-drying (DFD), freezing at −20 °C followed by freeze-drying (F20-FD), freezing at −80 °C followed by freeze-drying (F80-FD), and soaking in 5% vitamin C solution followed by freezing at −80 °C and freeze-drying (VC-F80-FD)—on total phenolic content (TPC) and total alkaloid content (TAC) were compared. PPO activity was highest in freshly collected samples (279.28 ± 12.61 U/g) and decreased significantly with decreasing freezing temperature and prolonged freezing time, whereas POD activity was markedly activated by prolonged freezing at −20 °C. Pre-freezing at −80 °C for 24 h followed by storage at −20 °C for 72 h gave the lowest PPO activity (117.28 ± 9.04 U/g), whereas short-term freezing at −80 °C better preserved native POD activity while significantly inhibiting PPO. Among the eight drying methods, freeze-drying generally gave a higher TPC and TAC than SD, OD-60, VD-40, and BF-FD when expressed per gram of extract. DFD was the most operationally simplified freeze-drying protocol among those tested, with a high total phenolic content per gram of extract and a relatively high phenolic content per gram of dry rhizome compared with the non-freeze-drying methods; however, its alkaloid content, like that of the freeze-dried samples in general, was not higher than that of SD on a dry-weight basis. Because fresh rhizomes could not be homogenized for parallel extraction, the TPC and TAC values represent relative differences among the drying methods tested rather than absolute contents or retention rates relative to the fresh material. UHPLC-ESI-Q-TOF-MS analysis detected 75 chromatographic features, for which 84 annotations were proposed (MSI Level 2–4), including phenolics, triterpenoid saponins, alkaloids, fatty acids, and their derivatives. Comparative analysis further revealed that eight components, including hydroxytyrosol 1-O-glucoside, were absent in the shade-dried sample, consistent with visible browning during SD and with the loss of specific phenolic components and a decline in TPC. These findings clarify the enzymatic basis of browning in Hylomecon japonica rhizomes and provide a scientific basis and new ideas for the harvesting, handling, and processing of this medicinal plant resource.