Cement roadbeds that have been in a natural environment for a long time are prone to thermal fatigue degradation due to temperature differences. In this paper, microbial technology is used to improve the highly weathered phyllite, and the optimal mix proportion is determined by orthogonal experiments. An environmental thermal fatigue test is performed on the enhanced samples, revealing how the pore structure of samples modified with various gelling liquids alters as the duration of thermal fatigue increases. By using low-field nuclear magnetic resonance and non-metallic ultrasonic detection technology, the thermal fatigue degradation mechanism of microbially modified strongly weathered phyllite filler is analyzed. The results show that the strength and anti-seepage performance of the filler after microbial improvement have been significantly improved, meeting the requirements of the project. Thermal fatigue increases the porosity and peak signal strength of the samples and increases the complexity of the pore size and its distribution more complex, leading to the coarsening of the pore structure and an obvious deterioration trend. The capillary fractal dimension of the sample decreases as the number of thermal fatigue cycles and pore ratio increase, and the sample modified with magnesium chloride is particularly sensitive to the thermal fatigue effect. The ultrasonic wave velocities of the samples all decrease, and the damage degree shows a significant secondary growth mode with increasing thermal fatigue cycles. Therefore, this paper recommends the use of calcium chloride as a gelling liquid in the actual projects to optimize the comprehensive performance of microbially modified strongly weathered phyllite fillers, effectively resist the potential impact of temperature stress fluctuations, and ensure the stability and durability of roadbeds. The research results not only provide a solid theoretical basis for the performance evaluation of roadbed fillers, but also indicate a direction for their scientific application in safety engineering.