Variation regularities of atomic interaction potentials of Ni-Al-Fe alloy based on the microscopic phase-field theory were investigated. The first nearest neighbor atomic interaction potentials of Ni-Al-Fe alloy’s L12 structure were inversed out according to the formula that illustrates the first nearest neighbor atomic interaction potentials of L12 structure alloy which was referenced on the relation equation between atomic interaction potentials and long range order parameters by Khachaturyan. The experimental results indicate that Ni-Al (WNi-Al) and Ni-Fe (WNi-Fe)’s first nearest neighbor atomic interaction potentials will increase linearly with the temperatures rising. WNi-Al increases but WNi-Fe decreases roughly linearly if Al atom’s concentration rises, and vice versa. The inversion potentials are inversed into microscopic phase-field equation, then getting a finer grain of atomic evolution pictures and a higher degree of long range order of structure.