In this study, to explore the microstructure deformation mechanism of marine soft marine soil under cyclic loading, we analyzed the dynamic properties of soft marine soil under cyclic loading via dynamic consolidation compression testing. Then, using Image-Pro Plus (IPP) 6.0 image analysis software, and according to the dynamic consolidation compression test results and the images from a scanning electron microscope (SEM), we determined the weakening effect of soft soils under different consolidation confining pressures, different cyclic stress ratios, and different over-consolidation ratios. After dynamic consolidation and compression, the pore structure of undisturbed soft marine soil tends to compact, the degree of soil particle fragmentation intensifies, small pores increase, large pores decrease, the pores become more regular, and the distribution of pores is directional. Subsequently, for undisturbed soft marine soil, the higher the consolidated confining pressure, cyclic dynamic stress ratio, and over-consolidation ratio, the greater the damage to the pore structure, and the more obvious the structural weakening effect exhibited under cyclic loading.