Phyllite is in a loose accumulation state after weathering, and there is a lack of suitable slag dump sites. The engineering properties of strongly weathered phyllite with poor strength and water stability can be improved by microbiological modification so that it is suitable for roadbed filling. This paper uses microorganisms to improve the strongly weathered phyllite filler, which does not conform to the hydrophysical properties of highway roadbed filler and studies the effects of different gelling fluids on the improvement. The spontaneous imbibition experiment is carried out on the modified sample to analyze the change rule of pore structure with time. The capillary water migration of the three sample groups is studied by using the nuclear magnetic resonance technique and finite element software. The results show that the carbonates produced by different gelling liquids have different particle encapsulation properties. After the calcium acetate improvement, the crystal content of calcium carbonate reached 20.5%. The pore ratio and equivalent average pore size of the three groups of samples increased with increasing spontaneous imbibition time. The fractal dimension of capillary pores is inversely proportional to the proportion of capillary pores. The capillary water absorption coefficient of the modified sample is 0.01. Both laboratory tests and numerical simulation results show that the improvement effect of calcium acetate is superior to that of the other two gelling liquids. The research results provide a reference for predicting the distribution of groundwater movement in strongly weathered phyllite modified by microorganisms as roadbed fillers.