<p>When exposed to natural environments for extended periods, strongly weathered phyllite subgrade fill materials are highly susceptible to drying–wetting cycles induced by rainfall, leading to progressive deterioration of mechanical performance. In this study, microbial-induced calcium carbonate precipitation technology was employed to improve strongly weathered phyllite fill materials. Drying–wetting cycling tests were conducted on both untreated and microbially treated samples. The evolution of pore structure, uniaxial compressive strength, and damage characteristics with increasing number of wetting–drying cycles was systematically investigated. Nuclear magnetic resonance, ultrasonic testing, and uniaxial compression tests were combined with an attenuation degree model and damage theory to elucidate the strength degradation mechanism under cyclic environmental loading. The results indicate that microbial treatment significantly refines the pore size distribution toward smaller diameters and reduces porosity, thereby increasing material compactness. Similarly, the uniaxial compressive strength and P-wave velocity increase, reflecting improved overall mechanical properties. With increasing number of wetting–drying cycles, the proportion of micropores gradually increases, whereas the number of mesopores decreases, the porosity increases steadily, the P-wave velocity and uniaxial compressive strength continuously decrease, the degree of damage increases logarithmically. In terms of all the evaluated aspects, the microbially treated samples consistently outperform the untreated control group, demonstrating superior resistance to deterioration induced by drying–wetting cycles. These findings confirm that MICP technology effectively enhances the durability and stability of strongly weathered phyllite fill materials under rainfall-induced drying–wetting cycles, providing a promising solution for improving subgrade performance under adverse environmental conditions.</p>