Amomum villosum (AMV), as a 1300-year-old medicine and food homology, has been lack of comprehensive quality evaluation for a long time. This study established the fingerprints of AMV by chromatographic, spectroscopic and thermal technologies and investigated the antioxidant activity to assess holistically the quality of 22 batches of AMV samples. GC-HPLC tandem fingerprints, FTIR and DSC quantum fingerprints were first developed respectively and fused for evaluating qualitatively and quantitatively, in which the contents of eight compounds were determined simultaneously. Especially, the equal-weight method was used to fuse the different analytical techniques mentioned above and to evaluate the quality of AMV samples with the help of systematically quantified fingerprint method. As a result, all samples were well differentiated and classified into five grades. Moreover, the correlation between the chromatographic fingerprint peaks and antioxidant activity was confirmed by the gray relational analysis. In summary, the proper fusion of multidimensional fingerprint techniques and multidimensional analytical techniques provides a reliable and comprehensive method for the evaluation of AMV and their related products.