Based on the empirical electron theory of solids and molecules theory(EET), the valence electron structures(VESs) of the strengthening phases Al3Fe and Al6Fe in Al-Fe alloy are calculated, then the stability of Al3Fe and Al6Fe, the precipitated sequence under the non-equilibrium solidification, the phase transition during aging and the effects of alloy elements are discussed. The results show that the values of covalent electron pairs on the strongest bond n1, the total forming bond ability F, and the number of atom state group σN of Al3Fe and Al6Fe are bigger than that of Mg17Al12 and Mg2Si, so the stability of Al3Fe and Al6Fe is better. The total forming bond ability of Al6Fe is far smaller than that of Al3Fe, so Al6Fe generates first under the equilibrium solidification. The strongest bond of Al6Fe is weaker than that of Al3Fe, so Al6Fe is easy to be broken up and form the more stable Al3Fe finally during aging. The addition of alloy elements changes the VES of Al6Fe and makes its values of F, σN and n1 increased, the stability of Al6Fe is strengthened too, which delays the Al6Fe→Al3Fe transition and improves the transition temperature.