The recent experimental and theoretical studies indicate that the heterogeneous dislocation cell structure in metal sample at micron scale plays a significance role in characterizing the size effect and stair-like fluctuation plasticity deformation. To reveal the essential connection between the dislocation cell structure and the unravel plasticity deformation behaviors, a dislocation-based continuum crystal plasticity model is proposed in this work to simulated the microcompression tests for micropillars at the different micron sizes. The heterogeneous distribution of the dislocations in the micropillar is formulated by the evolution equations of dislocation density of the dislocation cell and wall for the first time. It is confirmed that the cell size and wall thickness are correlated with the dislocation density in cell and wall. The microcompression simulation of the single crystal Ni sample at micron scale with diameter ranging from 2 and 20 μm is applied by the present model. The results reveal that the size effect of the flow stress not only depend on the dislocation cell size (DCS) and wall thickness (DWT), but also depend on the diameter of micropillar. The intermittent flow is attributed to the heterogeneous distribution of dislocations. It is also observed that the dislocation cell structure refinement phenomenon is apparent with the increase in plasticity deformation.