Calophaca sinica is a rare wild plant endemic to North China. To explore the nutritive value of C. sinica, the comparative metabolomics of C. sinica and Glycine max (as control group) seeds were studied by liquid chromatography-mass spectrometry (LC-MS). The results were as follows: (1) A total of 1 857 metabolites were detected in these two species, and 1 698 metabolites were similar in composition and content (>90%), and only 159 differential metabolites (