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In this study, molecular dynamics (MD) simulation is adopted to explore the mechanical properties and microstructure evolution of a dual-phase CoCrFeMnNi high-entropy alloy during nanoindentation. The influence of the volume fraction of the hexagonal closed-packed (hcp) phase is considered, and the P–h curves are plotted, where the indentation depths of curves initially into the plastic stage and the maximum indentation force for each curve are significantly different. At the elastic stage, the results from MD simulations are in agreement with those of the Hertz contact theory. However, the fitting coefficient k is remarkably influenced by the hcp phase volume fraction. The correlating P–h curves of plastic deformation are investigated by analyzing the instantaneous defect structures dominated by the nucleation of Shockley partial dislocations or the movements of stacking faults. Furthermore, the microstructure evolution with the increment in indentation depth is demonstrated, and it revealed that the plastic deformation is affected by the phase structure indenter that initially contacts. Unlike the slipping process for the face-centered-cube phase, a new hcp structure grain is created through dynamic recrystallization if the hcp phase is the first phase that the indenter touches.