The precipitates have a significant influence on fatigue behavior in magnesium (Mg) alloy. In this work, the effects of precipitates on deformation mode, cracking mode and mechanical behavior during low-cycle fatigue under stress-controlled mode in WE54 Mg alloy at room temperature (RT) was analyzed quantitively and statistically via quasi-in-situ electron backscattered diffraction (EBSD), slip trace analysis, coupled with transmission electron microscopy (TEM). The results reveal that precipitates promoted the activation of pyramidal < c + a > dislocation slip and suppressed the activation of tension twinning in the T6 alloy. In the T4 alloy, persistent slip band (PSB) induced cracking together with intergranular cracking dominated fatigue damage, while intergranular cracking was the primary cracking mode in the T6 alloy. The obvious cyclic hardening behavior of the T4 alloy was attributed to dynamic precipitation, whereas suppressed dynamic precipitation, restrained multiplication of dislocations, together with the appearance of PFZ generated the marginal cyclic hardening behavior in the T6 alloy. Both the T4 and T6 alloys exhibited ratcheting behavior, and precipitates suppressed ratcheting deformation in the T6 alloy. Moreover, the underlying mechanism for the higher fatigue resistance in the T6 alloy was also discussed.