This study focuses on the storage process of coffee beans, employing electron beam irradiation (EBI) to investigate the comprehensive effects of different irradiation doses on coffee beans and their storage process, including physicochemical indicators, microbial abundance, and flavor compounds. The results showed that a 2 kGy dose of EBI could effectively reduce the total number of bacteria, molds, and yeasts in green coffee beans (GCBs), while a dose of 4 kGy can completely inactivate the bacteria and maintain this effect for one month. Compared with the control sample that has not undergone processing by EBI (CK), the crude fat content of the irradiated samples decreased, accompanied by a significant increase in acid value. After 30 days of storage, compared with the CK-30 sample, EBI treatment significantly reduced both the moisture content and overall brightness value of GCB. The analysis of aroma compounds in roasted coffee beans (RCBs) revealed that substances related to Maillard reaction, caramelization reaction and sugar degradation, such as 2-Furanmethanol and acetic acid, changed in the irradiated samples, but had no significant effect on the characteristic components like caffeine and the aroma detected by the electronic nose. The obtained results provide a scientific basis for applying irradiation technology to the preservation of coffee beans.