Liquid nitrogen ultra-low temperature treatment is an efficient and safe method for extending the shelf life of food. Rapid freezing and repeated freeze-thaw treatments on both green and roasted coffee beans were carried out by liquid nitrogen. Sensory evaluation of flavor, analysis of physicochemical components, determination of non-volatile compounds such as chlorogenic acid derivatives, alkaloids, andminerals, and scanning electron microscopy, were used to study the effects of ultra-low temperatures on the non-volatile flavor quality and ultra-microstructure of coffee beans. The results indicated that roasting combined with ultra-low temperature treatment significantly reduced the content of most chlorogenic acid derivatives and γ-aminobutyric acid in coffee beans, while significantly increased the levels of citric acid, malic acid, lactic acid, and alkaloids. Ultra-low temperature treatment had no significant impact on the sensory flavor of roasted coffee beans. Pre-roasting rapid freezing of green coffee beans using liquid nitrogen significantly increased the acrylamide content. Scanning electron microscopy observations revealed that ultra-low temperature treatment did not cause significant changes in the gap width of green coffee beans, whereas internal filamentous connections formed in roasted coffee beans, and the gap width of repeatedly freeze-thawed roasted coffee beans decreased significantly. Mantel tests and Pearson correlation analyses showed that the richness of roasted coffee beans sensory indicators was significantly correlated with chlorogenic acid and other compounds, and balance was extremely significantly correlated with mineral elements Fe and Cu. It was concluded that liquid nitrogen ultra-low temperature treatment could extend the flavor preservation period of coffee beans, but also caused changes in the content of non-volatile flavor components and microstructure. These findings aimed to provide a theoretical basis and data support for the storage and preservation of coffee beans and the control of flavor quality.