Bioleaching of effective silicon represents a crucial method for the green and efficient utilization of coal tailings (CTs). However, the influence of heavy metals present in coal tailings on this process cannot be underestimated. This study investigates the effects of five high-concentration heavy metal elements (Pb, Zn, Cu, Cr, and Ni) in CTs on the biological characteristics and leaching processes of Bacillus mucilaginosus (B.M.). The results indicated that varying concentrations of heavy metal elements significantly influenced the bioleaching of effective silicon by B.M.. Kinetic analysis revealed that the leaching process predominantly adhered to a chemical reaction-controlled mechanism. Changes in the functional groups, mineral composition, and morphology of the CTs surface demonstrated that chromium and nickel exerted a negligible effect on leaching effectiveness, with effective silicon concentrations of 315.71 mg/L and 322.62 mg/L, respectively. The activity of B.M. induced surface erosion of CTs, disrupting the crystal structure of silicon-bearing minerals and facilitating the conversion of silicon in quartz and kaolinite to effective silicon. In contrast, lead, zinc, and copper significantly inhibited B.M., hindering effective erosion of CTs and resulting in lower effective silicon leaching concentrations of 129.65 mg/L, 142.68 mg/L, and 135.70 mg/L, respectively. Therefore, this study summarizes the effects of various heavy metal elements on the bioleaching of effective silicon by B.M., providing a scientific foundation for the environmentally sustainable utilization of CTs.