Ni-based single crystal line alloy is constituted with γ phase and γ' phase in the form of coherency. Since an indenter for two-phase coherent structure is bigger than the usual nano-scale indenter, the press location of indenter may be unclear in nanoindentation simulation. Both γ phase and γ' phase may be pressed initially, and the mechanical properties shown are different because of the initial press locations. The nanoindentation of Ni-based single crystal line alloys is simulated by molecular dynamics method. Two models are used to study about the hardness in [001] crystal orientation, one is the model γ /γ' with the initial indentation on γ phase, and the other is the model γ'/γ with the initial indentation on γ' phase. The influence of misfit dislocation at (001) interface on nanoindentation of the two models is analyzed using a center-symmetry parameter. Results show that the misfit dislocation shape of the two models are different after relaxation. Lomer-Cottrell dislocation occurs on (001) interface in the γ'/γ model. Before 0.930 nm press depth is reached, there is little change in the (001) interface misfit dislocation of the two models. Relationship between press load and press depth is similar for the two models, and it is the same in the relationship between hardness and press depth. After press depth reaches 0.930 nm, the misfit dislocation at (001) interface for model γ'/γ grows big, which results in a smaller press load and a smaller hardness computation in the model γ'/γ than that in model γ /γ'. When the press depth reach 2.055 nm, we find only a small amount of dislocations in γ phase that can go into γ' phase since the misfit dislocation at (001) interface in model γ /γ' hinders the process. However, none of dislocations can go into γ phase because of the prevention caused by Lomer-Cottrell dislocation at the (001) interface in the model γ'/γ . That means the Lomer-Cottrell dislocation reinforces the material obviously. So the press load in model γ'/γ grows faster than that in model γ /γ'.