Edible flowers have been used in the food and beverage industries because of their high nutritional value, flavor, and scent. For the storage of edible flowers used in these industries, drying is a necessity to store the materials more easily and prevent the damage of metabolites in the flowers. However, drying may affect metabolite retention because drying conditions can differ according to the various methods. In this study, Agastache rugosa flowers were dried using four different methods (oven drying at 25 ± 1 °C, 50 ± 1 °C, 80 ± 1 °C, and freeze drying) and primary and secondary metabolites were analyzed using high-performance liquid chromatography (HPLC) and gas chromatography time-of-flight mass spectrometry (GC-TOF/MS). Freeze-dried flower samples contained higher levels of carotenoids (lutein, 13Z-β-carotene, β-carotene, and 9Z-β-carotene) and phenolics (rosmarinic acid, ferulic acid, and sinapic acid). Contrarily, the 80 °C oven-dried flower samples contained higher levels of most amino acids and flavonoids (including acacetin and tilianin) and at 25 °C and 50 °C contained higher levels of carbohydrates. Therefore, freeze-drying is a suitable method for retaining carotenoids and phenolics. In contrast, oven drying at 50 °C was highly recommended to retain amino acids and flavonoids.