Headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS) was used to study the effects of four kinds of probiotics on the volatile components of fermented coffee. The fingerprints showed that 51 compounds were confirmed and quantified, including 13 esters, 11 aldehydes, 9 alcohols, 6 ketones, 3 furans, 5 terpenes (hydrocarbons), 2 organic acids, 1 pyrazine, and 1 sulfur-containing compound. After fermenting, the aroma of the green beans increases while that of the roasted beans decreases. After roasting, the total amount of aroma components in coffee beans increased by 4.48–5.49 times. The aroma differences between fermented and untreated roasted beans were more significant than those between fermented and untreated green beans. HS-GC-IMS can distinguish the difference in coffee aroma, and each probiotic has a unique influence on the coffee aroma. Using probiotics to ferment coffee can significantly improve the aroma of coffee and provide certain application prospects for improving the quality of commercial coffee beans.