The strain-controlled cyclic deformation behaviour of Mg-9Gd-4Y-2Zn-0.5Zr with different structures was investigated. Alloys were prepared by solution, extrusion and pre-ageing extrusion, and the microstructures before and after the fatigue tests were characterized. Experimental results indicated that the bimodal structure owned the better performance in fatigue test, which was attributed to the higher yield strength. For the equiaxed structure, cyclic hardening induced stress concentration until the failure. Stable cyclic deformation and persistent cyclic softening played an important role at the low and high strain amplitudes, respectively. This was attributed to the formation of fine grains relieving the stress concentration during cyclic loading. In addition, residual twins were observed in equiaxed structure to induce crack, and the bimodal structure effectively restrain it.