Abstract: To address the challenge of poor compatibility between fracturing fluid thickeners and microbial metabolism in biogenic coalbed methane (CBM) reservoir stimulation, this study developed a multidimensional evaluation system encompassing gel-breaking efficiency, pore structure modification, and metabolic activation. Using this framework, the synergistic mechanisms of methane enhancement by three thickeners—guar gum, xanthan gum, and modified cellulose—were systematically compared. Gel-breaking agents comprising microbial consortia and ammonium persulfate were used to assess the viscosity degradation kinetics of the thickeners at 0.4% concentration. Xanthan gum and guar gum exhibited superior viscosity reduction, with final viscosities of 3.5 mPa·s and 2.3 mPa·s after 60 hours, significantly outperforming modified cellulose (4.8 mPa·s). Polyacrylamide was excluded due to its resistance to biodegradation, with a residual viscosity of 8.6 mPa·s. Anaerobic co-fermentation experiments with lignite and thickeners revealed that the xanthan gum system achieved a cumulative gas production of 321 mL, representing increases of 40.8% and 205.7% over guar gum and modified cellulose, respectively. Improved Gompertz model fitting indicated a maximum gas production potential 4.7 times that of the control lignite group. Pore structure characterization showed that xanthan gum reduced the specific surface area of lignite by 28.4% and expanded the mesopore volume to 0.047 cm³/g. Fourier transform infrared spectroscopy (FTIR) analysis confirmed its role in promoting the cleavage of aliphatic chains and aromatic structures, thereby releasing soluble organic matter. Three-dimensional fluorescence spectroscopy further revealed that xanthan gum increased the content of soluble organic matter in the fermentation broth, providing sufficient substrates for microbial metabolism. Metagenomic analysis demonstrated that xanthan gum specifically enriched the aceticlastic methanogen Methanothrix and significantly upregulated the acetate decarboxylation pathway. The expression level of the key gene K00925 reached 356.8, notably higher than that in the guar gum system (259.9). Moreover, the total abundance of related functional genes increased by more than 20%. This study established a multidimensional evaluation framework integrating gel-breaking performance, pore structure modification, and metabolic activation, elucidating the structure–function relationship of thickener–microbe synergy. The results demonstrate that xanthan gum enables simultaneous optimization of reservoir physical properties and reconstruction of microbial metabolic networks, offering theoretical and technical support for the development of bio-compatible fracturing fluids.