The incompatibility of plastic deformation in a near β titanium alloy with (α β) two phases microstructure was analyzed based on the crystal plasticity finite element (CPFE) model. The bicrystal simulation results show that the plastic deformation in the microstructure with (α β) two phases is incompatible, wherein the deformation behavior of α phase is significantly affected by the crystal orientation and loading direction. In addition, by coupling with three-dimensional (3D) Voronoi tessellation (VT) geometric model, the effect of globular primary α phase in the β matrix on the macroscopic mechanical response was discussed. Based on the CPFE-VT model, it is found that the incompatibility of plastic deformation between the α and β phases results in a linear reduction of the macroscopic strength with the proportional increasing of volume fraction of α phase which has a lower critical resolved shear stress. Furthermore, the distribution of primary α phase also has a significant effect on the stress-strain response. The proposed model for near β titanium alloy with dual phase microstructure yields important information for the microstructure controlling and the performance prediction.