Although Lilium brownii (L.brownii) bulbs are popular fresh vegetables, a series of quality problems still remain after harvest. In this study, fresh L.brownii bulbs were placed in the dark at 25, 4, and −20 °C and under light at 25 °C from 0 to 30 days; the chemical compositions were analyzed by ultraviolet spectrophotometry (UV) and high-performance liquid chromatography quadrupole time-of-flight mass spectrometry (HPLC-Q-TOF-MS). During the 30-day storage period, the browning degree increased over the storage time and with increasing temperature, but the contents of proteins and free amino acids decreased and were aggravated by light. The total polyphenol content increased until the 6th day at 25 °C (dark or light), but it did not significantly accumulate at −20 or 4 °C. The reducing sugar content showed a dynamic balance, but the total polysaccharide content decreased constantly in the four storage conditions. The polyphenol oxidase (PPO) activity increased with storage time and increasing temperature, while it was inhibited by light. The increase rates of malondialdehyde (MDA) content at −20 °C and light (25 °C) were higher than those at 4 and 25 °C. In addition, 12 secondary metabolites were identified, most of which accumulated during the storage period, for example, 1-O-feruloyl-3-O-β-D-glucopyranosylglycerol; 1,3-O-di-p-coumaroylglycerol; 1-O-feruloyl-3-O-p-coumaroylglycerol; and 1,2-O-diferuloylglycerol. The variations in nutrient levels had a low correlation with browning, but the variations in MDA, PPO, and secondary metabolite (phenolic acids) levels had a high correlation with browning. In conclusion, fresh L.brownii bulbs should be stored at a low temperature (4 °C) and in dark condition, and browning bulbs are excellent materials for secondary metabolite utilization.