In the present study, a novel microbial nanocomposite "Paecilomyces lilacinus-silica nanoparticlescalcium-alginate beads" (P. lilacinus-SN-Cal-Alg) were synthesized and their high efficiency for removing Pb(II) ions was demonstrated in aqueous solution. P. lilacinus-SN-Cal-Alg beads before and after the adsorption of Pb(II) were characterized by FT-IR, SEM-EDS, and XPS analyses. The adsorption capacity of Pb(II) by P. lilacinus-SN-Cal-Alg beads was analyzed in aqueous solution. For comparison, the adsorption capacity of Pb(II) by another type of microbial composites, namely, P. lilacinus-Cal-Alg beads, without addition of silica nanoparticles, was also studied in parallel. Lastly, the equilibrium data in adsorption process were examined by both Langmuir and Freundlich isotherm models to evaluate adsorption mechanism. The results showed that an excellent removal efficiency of Pb(II) in aqueous solution (85.54%) was obtained at initial concentration of 200 mg/L by using the P. lilacinus-SN-Cal-Alg beads. Meanwhile, they exhibited the better adsorption capacity for Pb(II) than P. lilacinus-Cal-Alg beads. The adsorption process by P. lilacinus-SN-Cal-Alg beads was best described by the Langmuir model indicating that monolayer adsorption of Pb(II) ions takes place on the beads surfaces and showed that its maximum adsorption capacity was 282.49 mg/g.