• The fingerprints of Pu-erh tea were constructed by GC-E-Nose, GC–MS and GC-IMS. • Significant changes in the volatile components occurred over 3-year-storage time. • A clear discrimination was achieved based on the volatile metabolites with GC-IMS. • Nine volatile biomarkers were identified based on VIP＞1.2 and p＜0.05.