Seed fennel is one of the important spices 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 fertility varieties （FvGZKY001） of Guizhou province. We observated and identificated the sterility characters of FvGZBY001， and analyzed the difference of lipid composition between the two grains by LC-MS （liquid chromatography-mass spectrometry）. The results show that there was no significant difference in plant morphology in FvGZBY001 compared with the fertile material FvGZKY001， the filaments of FvGZBY001didnot 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 lipid substance 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） while 12 lipids was up-regulated expression in FvGZKY001 （mainly glycerol phospholipids）. LION enrichment analysis showed that 41 lipid substances with significant differences were mainly concentrated in 22 different lipid substances， which the predominant lipid substances were fatty acids with different carbon numbers. We presumed that fennel FvGZBY001 is NMS （nuclear male sterility）， and the sterility characteristics can be used in crossbreeding of fennel. The difference of lipid composition with FvGZKY001 can be used for the quality evaluation and utilization of its seed oil.