In this study, coffee samples from seven primary processing methods—traditional dry processing (CG), dry processing I (GA), dry processing II (GB), traditional wet processing (CS), honey processing I (MA), honey processing II (MB), and honey processing III (MC)—underwent comprehensive investigation using HS-SPME/GC-MS and HS-GC-IMS. A total of 81 and 96 VOCs were identified by GC-MS and GC-IMS, respectively. The differences in VOCs among various primary processing samples were observed. The results demonstrated increased volatilization of coffee flavor substances due to anaerobic fermentation. CG, GA, and GB samples exhibited high levels of fruity, floral, and sweet aromas. Conversely, honey processing methods (MA, MB, and MC) enhanced the caramel, roasted aroma, and buttery flavor of coffee samples. PCA and PLS-DA successfully categorized coffee beans based on their aroma properties. These findings indicated that honey processing, combined with drying, significantly influenced coffee bean VOCs, enhancing caramel, roasted aroma, and buttery flavor—crucial for the characteristic volatile metabolites of Yunnan arabica coffee beans.