FCC-structured CoCrFeMnNi high entropy alloy (HEA) has attracted abroad interests for years because of its excellent mechanical properties, except for strength. Recent experiments have reported a kind of nano-laminated dual-phase (NLDP) FCC/HCP structure that can strengthen the HEA. However, it is still unknown why the HEA can be strengthened by this kind of NLDP structure. Here, we employ molecular dynamics simulations to study the atomistic strengthening mechanism of the NLDP HEA. Dislocation-assisted multiple plastic deformation mechanisms in both FCC and HCP single phase HEAs are observed, and amorphization is also found in the plasticity of HCP phase, which are consistent with the previous experimental characterizations. The HCP phase possesses higher strength because of its higher stacking fault energy, higher Peierls–Nabarro stress and less active dislocation slip systems. It is also found that the introduction of HCP phase can enhance the mechanical properties, including yield stress, yield strain and plastic flow stress, of the NLDP HEAs, which also show volume fraction dependence. And the phase boundary plays crucial roles in the deformation and strengthening of the NLDP HEAs. The plastic deformation of the NLDP HEAs can be divided into two stages, i.e. stage I (plasticity only appears in FCC lamella) and stage II (plasticity in both FCC and HCP lamellas). With the increase of volume fraction, the lamella thickness of FCC matrix phase decreases, leading to continuous strengthening of yield properties and flow stress of stage I because of suppressed dislocation nucleation and confined dislocation motion in FCC matrix phase by the phase boundary. While there is no monotonous relationship between the flow stresses of stage II and the increasing volume fraction of HCP phase, which can be attributed to the competitive mechanisms between strengthening effect of phase boundary on the dislocation motion in FCC phase and softening effect of phase boundary on the dislocation motion in HCP phase. The results should be helpful for understanding the underlying physical mechanism of strengthening of HEAs with NLDP structure.