Amino acids are environment friendly organic inhibitors for most metals. The study on adsorption behavior of inhibitor molecules on metal surfaces has profound theoretical significance in understanding the anticorrosive mechanism and designing novel corrosion inhibitors. Based on first principles approach, the adsorption behaviour of three amino acid molecules (i.e., glycine, alanine, and leucine) on iron surface was studied in linear combination of atomic orbitals method with the Dmol3 package. Firstly, the morphology parameters of iron crystal surface were calculated, and then a suitable crystal face was chosen as the adsorption surface. Finally, some parameters including adsorption energy and projected density of states were calculated to explain the inhibition mechanism. The Fe(110) surface was an optimal simulation surface among the three common faces. Three molecules exhibited vertical adsorption structure on Fe(110) surface. The absolute values of adsorption energy were 2.233 eV, 2.254 eV, and 2.472 eV for glycine, alanine and leucine, respectively. The results were consistent with rank of experimental inhibition efficiency. The adsorption can reduce work function value of Fe(110) substrate. The Hirshfeld charge analysis shows that there is an electronic transfer process from the inhibitors to Fe substrate in all chemisorbed configurations. The analysis of state density suggests that several covalent bonds are formed between active atoms and Fe surface atoms in amino acid molecules. Bond energy plays a decisive role in the inhibitive efficiency of corresponding inhibitors.