Inhomogeneous gradient nanocrystals have better mechanical properties than uniform gradient nanocrystals. The segregation of solute elements in inhomogeneous gradient nanocrystals is expected to induce the re‐enhancement of mechanical properties of alloys. Herein, solute element segregation structures of inhomogeneous gradient structure nanocrystalline NiCo alloy are established, simulating tensile deformation via molecular dynamics. The results show that the segregation of solute elements in the inhomogeneous gradient structure of nanocrystals can improve the mechanical properties of the alloy, especially the structure of the intragranular segregation. The intragranular segregation of solute elements induces the decrease of grain boundary energy and greatly enhances the stability of grain boundaries. In addition, the segregation of solute elements within grains can hinder the dislocation movement to a certain extent, and the hindering effect on dislocation movement of stable grain boundaries induced by intragranular segregation of solute elements further enhances the mechanical properties of nanocrystalline alloys. This strategy of combining heterogeneous gradient structure and solute element segregation structure provides a positive and interesting perspective for the design of advanced alloys with excellent properties.