Abstract: The low utilization rate and poor water stability of strongly weathered phyllite in subgrade engineering present significant challenges in hot-humid regions of southern China. This study introduces microbially induced carbonate precipitation (MICP) technology combined with cement for improvement.. Through a three-factor, four-level orthogonal experimental design, the effects of bacterial solution concentration, coarse aggregate content, and cement content on the mechanical and permeability properties of the improved filler were systematically investigated. The results determined the optimal mix ratio: bacterial solution 0.05%, coarse aggregate 20%, and cement 15%. Under this optimal ratio, the unconfined compressive strength of the filler reached 7.35 MPa, representing a 72% increase compared to the control group without microbial treatment. Simultaneously, the permeability coefficient was significantly reduced to 2.651×10^-8 m/s, meeting the subgrade filler standard for secondary highways. Microscopic analysis reveals that the MICP process forms a composite cementation structure combining “coating-type” and “bridging-type” morphologies. The precipitates exist in the forms of calcite, aragonite, and vaterite, effectively filling pores and enhancing interparticle bonding. This study provides a theoretical basis and technical pathway for the resource utilization of phyllite. This study provides a theoretical basis and a viable technological pathway for the resource utilization of strongly weathered phyllite in road engineering.