To understand the structural origin of the significant improvement on the plasticity of Fe-based bulk metallic glasses (BMGs) through the replacement of Fe by Ni, the short-range order (SRO) and medium-range order (MRO) structures of Fe80−xNixP14B6 (x = 0, 20, 30, 40, 50 at.%) amorphous alloys are investigated by ab initio molecular dynamics (AIMD) simulation in the present work. It is found that the substitution of Ni for Fe causes the significant change in the local environment of B atoms. As the Ni replaces the Fe, the number of BB bonding decreases, and the fraction of ⟨0 3 6 0⟩ polyhedron decreases and that of ⟨0 2 8 0⟩ polyhedron increases among the major B-centered VPs. Additionally, the average coordination number (CN) of the present Fe-Ni-P-B amorphous alloys decreases with increasing the Ni content. The decrease of the number of BB bonding and the average CN are conducive to plastic deformation, which may be responsible for the improvement on the plasticity of the present Fe-Ni-P-B amorphous alloys through the Ni addition. The bond pair analysis indicates that, with the increase of Ni content, the fraction of 15xx bond pair with a five-fold symmetry and the number of pentagons decrease, and that of 1431, 142x and 1311 bond pairs of non-fivefold symmetry increase in the present Fe-Ni-P-B amorphous alloys, indicating that the reduction of fivefold symmetrical SRO is benefit to the intrinsic plasticity. The MRO investigation indicates that, as increasing the substitution content of Ni for Fe, the vertex-shared connection increases and the edge-shared connection decreases, which result in the increase of cavity and boundary between the SRO atomic clusters, and thus will be conducive to the improvement of the plasticity of the present Fe-Ni-P-B amorphous alloys.