Objective To investigate the influence of two microwave drying methods on the content of ethanol-soluble extracts, chlorogenic acid, and total flavonoids in Flos Mume, and to provide a basis for establishing new methods for processing of Flos Mume in producing areas. Methods Fresh Flos Mume samples were treated by direct microwave drying or drying after microwave fixation. With ethanol-soluble extracts, chlorogenic acid, and total flavonoids as assessment indices, their content was measured to investigate the influence of different drying methods on the quality of Flos Mume. A comparative analysis was performed between these samples and those processed in producing areas. Results There was a significant difference in the influence on the quality of Flos Mume between the two microwave drying methods. Drying after microwave fixation was better than direct microwave drying and obtained a color of yellow green in calyx, better appearance properties, and higher content of chlorogenic acid and total flavonoids. The optimal process of microwave drying was as follows: Flos Mume samples were placed in a microwave tray, sealed with a film, and microwaved for 2 minutes at 90 ℃, and then the film was removed and the samples were placed in air for 2 minutes; next, the samples were spread out on the tray and microwaved for another 10 minutes at a temperature of 50 ℃. Conclusion Different microwave drying methods have great influence on the content of effective constituents in Flos Mume.