A novel approach to mitigate the environmental concerns associated with cement industry is to replace Portland cement with low carbon alternative materials such as fly ash-based geopolymer cement. Hence, reactive MgO-activated low-calcium Class F fly ash was employed in comparison to Na2SO4-activated fly ash to stabilize a lacustrine soil reused potentially in soft coastal reclamation projects and as reinforced aggregates for anti-corrosion in marine engineering. The microstructural and strength properties were investigated with series of tests including X-ray diffraction (XRD), thermogravimetry/differential thermogravimetry (TG/DTG), mercury intrusion porosimetry (MIP), scanning electron microscopy (SEM), and unconfined compressive strength (UCS). The results demonstrate that the main hydration products in reactive MgO- and Na2SO4-fly ash-solidified soils are, respectively, magnesium silicate hydrate (M-S-H) gel and sodium aluminosilicate hydrate (N-A-S-H) gel. This finding is reconfirmed by the weight loss of solidified samples at 40–200 °C, which is correspondingly attributed to the dehydration of magnesium silicate hydrate (M-S-H) gel and sodium aluminosilicate hydrate (N-A-S-H) gel. The morphology and bonding ability of hydration products affects the microstructure and long-term strength of solidified soils. The microstructural change identified from SEM images coincides well with the quantitative evolution of pore structure. The pores with radius of 0.01–1 µm, i.e., micropore and mesopore, are supposed to be the dominant pores in reactive MgO- and Na2SO4-activated fly ash-solidified soils. The comparison of UCS indicates reactive MgO-activated low-Ca fly ash behaves much superior to Na2SO4-activated fly ash in enhancing the long-term compressive strength of soils. This study provides insight into the promising potential of low-Ca fly ash activated by immerging material–reactive MgO to replace cement in soil improvement