A mesoscale dislocation dynamics model which couples three-dimensional dislocation dynamics (DD), and finite element method (FEM) was used to investigate the mechanical response of Aluminum (Al) single crystal under spherical nanoindentation. Together with an atomistically informed nucleation model, the dislocation dynamics model can capture both the dynamic evolution of dislocations under the complex stress state of indentation and the corresponding constitutive response of material. The resulting load-displacement curves and the evolution of dislocation microstructures were analyzed to provide insights into the underlying deformation mechanism for incipient plasticity under nanoindentation. Our model could show the transition of the governing mechanism for plasticity from nucleation-controlled plasticity to pre-existing source-driven plasticity with increasing indenter size, as shown in recent experiments. In addition, it could capture a clear picture on incipient plasticity including the formation of prismatic loops through successive cross-slips of nucleated dislocations, such as rhombus loop and prismatic helical structures, which agrees well with atomistic modeling results.