The microbial flocculants (MBFs) hold the potential of biosorption to removal the heavy metals. However, it remains unclear what the relationship between biosorption and bioflocculation. Here, during the hydroxide precipitation of Cu, Zn, Pb and Cd, besides the commonly used pH, a three-phase division of zeta potential curves provided an orientation for the addition of MBFs. The plateau phase of zeta potential, indicating an insufficient hydroxide precipitation, was appropriate for introducing MBFGA1, a polysaccharide-based MBF. Its removal capacities on Cu, Zn, Pb and Cd reached the highest of 250 mg/g, 96.7 mg/g, 551.1 mg/g and 233.3 mg/g, respectively. A sufficiently suspended hydroxide precipitates of Pb could receive a higher dosage of MBFGA1, ensure their thorough separation, and finally improve the removal efficiency. In order to further control the residual risk of MBFGA1, the response surface methodology (RSM) was employed to optimize this process. The compromised results improved the Pb removal rate to 98% in a weak acidic solution at pH 6.2. The precipitates composition and crystallinity, the functional groups and the molecular morphology were characterized by the X-ray diffraction (XRD), fourier transform-infrared spectra (FTIRs) and atomic force microscopy (AFM), respectively. The results indicated that the negatively-charged hydroxyl, carbonyl, amino and phosphoryl played the significant roles on fixing the molecular of MBFGA1 on the precipitates, providing the points for the aggregation of flocs, and capturing the residual Pb ions. The insufficient hydroxide precipitation laid the foundation for these multiple functions of MBFGA1, and promoted the synergistic effects between biosorption and bioflocculation.