Terahertz metasurface sensors have attracted great interest in recent years due to their fast and non-destructive detection. One of the main research hotspots is to further improve sensing sensitivity, i.e., to achieve accurate discrimination with minimal amounts of marker targets for fast disease diagnosis. Graphene is a two-dimensional material with unique properties, for example, its electrical properties can be manipulated by the contact biomolecules, providing excellent sensing performance. In this paper, a metal-graphene hybrid metasurface is proposed and demonstrated for high-sensitive biosensing based on the plasmon-induced transparency (PIT) resonances. Experimental results show that 0.8 ng of the tyrosine enhances the PIT window to 4.8-fold, with the limit of detection down to 10 ng/mL. And with increasing amino acid quantities, three amino acids can be high-effectively distinguished to diagnose tyrosinemia, phenylketonuria, and hyperglycinemia. This metasurface sensor has the advantages of high sensitivity, fast detection speed, label-free and steady properties, which has potential applications in the fields of trace molecular sensing and disease diagnosis.