Seed fennel is one of the importantspices in Chinese marinade and barbecue. The lack of male sterile material severely limits the research process of breeding high-quality seed fennel varieties. In this study, male sterile materials (FvGZBY001) of seed fennel were obtained from local fertilityvarieties (FvGZKY001) of Guizhou province. We describedthe sterility characters of FvGZBY001, and analyzed the difference of lipid composition between the two grains by Liquid Chromatography-Mass Spectrometry (LC-MS). The results show thatthere was no significant difference in plant morphology both FvGZBY001 and FvGZKY001, the filaments of FvGZBY001did not extend significantly and no pollen grains in anthers. There were 7 types of 49 lipid molecule subclasses detected in the seeds fennel both FvGZBY001 and FvGZKY001, which are 1353 and 1351 kinds of lipidsubstance respectively. A total of 41 lipid substances with significant differences were identified among them, which 29 lipids were up-regulated expression in FvGZBY001 (mainly sphingomyelin) while12 lipids was up-regulated expression in FvGZKY001 (mainly glycerol phospholipids). LION enrichment analysis showed that they were mainly concentrated in 22 different lipid substances, which thepredominant lipid substances were fatty acids with different carbon numbers. So the sterility characteristics of fennel FvGZBY001 can be used in crossbreedingof fennel, and the difference of lipid composition from FvGZKY001 can be used forthequality evaluationand utilization of the oil extracted from their seeds.