Sulfate soils often caused foundation settlement, uneven deformation, and ground cracking. The distribution of sulfate-bearing soil is extensive, and effective stabilization of sulfate-bearing soil could potentially exert a profound influence on environmental protection. Ground granulated blast furnace slag (GGBS)–magnesia (MgO) can be an effective solution to stabilize sulfate soils. Dynamic cyclic loading can be used to simulate moving vehicles applied on subgrade soils, but studies on the dynamic mechanical properties of sulfate-bearing soil under cyclic loading are limited. In this study, GGBS-MgO was used to treat Ca-sulfate soil and Mg-sulfate soil. The swelling of the specimens was analyzed by a three-dimensional swelling test, and the change in compressive strength of the specimens after immersion was analyzed by an unconfined test. The dynamic elastic properties and energy dissipation of GGBS-MgO-stabilized sulfate soils were evaluated using a fatigue test, and the mineralogy and microstructure of the stabilized soils were investigated by X-ray diffraction and scanning electron microscopy. The results showed that the maximum swelling percentage of stabilized Ca-sulfate soil was achieved when the GGBS:MgO ratio was 6:4, resulting in an expansion rate of 14.211%. In contrast, stabilized Mg-sulfate soil exhibited maximum swelling at GGBS:MgO = 9:1, with a swelling percentage of 5.127%. As the GGBS:MgO ratio decreased, the dynamic elastic modulus of stabilized Ca-sulfate soil diminished from 2.8 MPa to 2.69 MPa, and energy dissipation reduced from 0.02 MJ/m3 to 0.019 MJ/m3. Conversely, the dynamic elastic modulus of stabilized Mg-sulfate soil escalated from 2.16 MPa to 6.12 MPa, while energy dissipation decreased from 0.023 MJ/m3 to 0.004 MJ/m3. After soaking, the dynamic elastic modulus of Ca-sulfate soil peaked (4.01 MPa) and energy dissipation was at its lowest (0.012 MJ/m3) at GGBS:MgO = 9:1. However, stabilized Mg-sulfate soil exhibited superior performance at GGBS:MgO = 6:4, with a dynamic elastic modulus of 0.74 MPa and energy dissipation of 0.05 MJ/m3. CSH increased significantly in the Ca-sulfate soil treated with GGBS-MgO. The generation of ettringite increased with the decrease in the GGBS-MgO ratio after immersion. MSH and less CSH were formed in GGBS-MgO-stabilized Mg-sulfate soil compared to Ca-sulfate soils. In summary, the results of this study provide some references for the improvement and application of sulfate soil in the field of road subgrade.