Asparagus is a perennial herb and is widely used as food and medicine in China. In this study, untargeted metabolomics analysis was applied to compare the chemical differences between the edible and inedible parts of asparagus, as well as the inedible parts of white and green asparagus. A total of 342 compounds were identified in the asparagus extracts, and 24 steroid saponins, 31 oxylipins and 36 LysoGPLs were identified for the first time in asparagus. Metabolomics analysis showed that the inedible part of white asparagus is rich in steroidal saponins, oxylipins and alkaloids, while the inedible part of green asparagus is rich in flavonoids, phenolic acids, LysoGPLs and amino acids. The inedible part of white asparagus showed significantly higher inhibitory effects on breast cancer 4T-1 cells than that of green asparagus. Network pharmacology analysis and molecular docking showed that the biological difference is related to higher levels of steroidal saponins and oxylipins in the inedible part of white asparagus. This study is useful for the wasted resource utilization of inedible parts of asparagus.