Celery seeds contain various bioactive compounds and are commonly used as a spice and nutritional supplement in people’s daily lives. The quality of celery seeds sold on the market varies, and their regions of production are unclear. This study evaluated the metabolites of Chinese celery seeds from three production regions using HS-SPME-GC-MS, HS-GC-IMS, and UPLC-ESI-MS/MS. The results indicate that GC-IMS analysis obtained a metabolic profile different from that detected using GC-MS. Terpenoids, polyphenols, coumarins, and phthalides are the main bioactive compounds in celery seeds. The production region significantly affects the metabolic characteristics of celery seeds. Based on GC-MS data, GC-IMS data, and LC-MS data, the variation analysis screened 6, 12, and 8 metabolites as potential characteristic metabolites in celery seeds related to the production region, respectively. According to the aromatic characteristics of the characteristic metabolites, seeds from the HCQ region and HZC region have a strong herbal, woody, celery, and turpentine aroma. The concentration of secondary metabolites was highest in the seeds from the HCQ region followed by the HZC region, and it was the lowest in the JJC region. Altogether, this study investigates how geographical origins influence the metabolomic profile of celery seeds. The results can be used to guide the planting and harvesting of celery seeds in suitable regions.