Solute element segregation behavior significantly changes the mechanical properties and deformation mechanism of nanocrystals. In this work, we studied the effect of segregation structure on the deformation mechanism of NiCoAl nanocrystalline by molecular dynamics. The results show that the grain boundary stability of nanocrystals is the worst when Al is completely segregated within the grain, and the metastable grain boundary cannot effectively hinder the dislocation movement, resulting in poor mechanical properties of nanocrystals. When 4% of Al transitioned to the grain boundary, the grain boundary stability was greatly improved and many lamination structures were generated. At this time, the lamination structure and stable grain boundaries were effectively nailed to dislocations, resulting in nanocrystal strengthening. With the complete segregation of Al at the grain boundary, the grain boundary shows a stable ability significantly and inhibits the nucleation of dislocation, leading to a decline in the strength of nanocrystals. In this effort, the deformation mechanism of solute element segregation is investigated from the interaction of dislocation and solid solution element, which is conducive to the design of advanced materials with excellent properties. Our work provides fascinating insights into the mechanism of plastic deformation response under solute element segregation structure.