As the lightest metal structural material, magnesium alloy is known as the “green engineering material” of the 21st century. Especially, crystalline-amorphous dual-phase nanostructure magnesium materials exhibit excellent mechanical properties, though the mechanism of interaction between the dislocation in crystal and amorphous phase is still under the investigation. In the present work, the interaction between the edge dislocation and amorphous phase in nanocrystalline magnesium under shear load is studied by using molecular dynamics simulation. The result indicates that the interaction mechanism between amorphous phase and dislocation shows the size dependence. Compared with the sample with smaller amorphous size, larger amorphous size will lead to a large second strengthening effect. And the mechanism of the interaction between amorphous phase and dislocation is mainly attributed to the pinning effect of amorphous on the dislocation. For the samples with small amorphous size, the pinning effect of amorphous on the dislocation is limited and the pinning time is shorter. The interaction mechanism is contributed mainly by the dislocation bypassing amorphous phase. While for the samples with larger amorphous size, the pinning effect of amorphous on the dislocation is larger and the pinning time is longer. The interaction is due mainly to the cross slip mechanism of dislocation caused by amorphous phase. The results from this work have a certain reference value and guiding significance for designing and preparing the high-performance magnesium and its alloys.