This study evaluated the effects of three storage temperatures (4 °C, −20 °C, −80 °C) on metabolites in saffron stigmas after one year of storage using non-targeted metabolomics based on LC-MS and GC-TOF-MS. Lower storage temperatures better preserved chemical activity, and different metabolites markedly included capsiate, sarmentine, sesamolinol, nobiletin, prostaglandin F1α, vanillin, and α-ketoglutaric acid. Amino acid-centered pathways, including alanine, aspartate, glutamate, and phenylalanine metabolism, constitute core temperature-responsive modules. Aspartic acid and alpha-ketoisovaleric acid exhibited strong correlations with key quality indicators crocin and picrocrocin. The −80 °C treatment significantly yielded the highest retention of crocin and picrocrocin, with their contents being 21.46% and 31.25% higher, respectively, than at 4 °C. −80 °C is recommended for long-term storage, whereas −20 °C is suitable for household use. This study provides a theoretical foundation and practical guidance for saffron preservation for producers and consumers.