Glomalin-related soil protein (GRSP), a microbial product that can be used as a bioflocculant, is critical to metal sequestration in the ecosystem. However, the relationship between GRSP and heavy metal has not been well explored. In this study, the adsorption behaviors and mechanisms of Pb(II) and Zn(II) ions on GRSP were investigated. Results reveal that the Pb(II) and Zn(II) adsorption closely conform to the pseudo second-order model, which indicates that the chemisorption of GRSP occurred after intra-particle diffusion. The adsorption process is influenced by the degree of pollution, pH value, GRSP content in the environment. In addition, scanning electron microscopy coupled with microanalysis (SEM-EDX) reveals that the surface structure of GRSP is irregularly blocky or flaky and metal ions are uniformly distributed on the surface of GRSP. Fourier transform infrared (FT-IR), X-ray photoelectron spectroscopy (XPS), and X-ray diffraction (XRD) analysis show that the carboxyl and nitro groups on GRSP act as ligands to form complexes with two divalent metal ions. The interaction between GRSP and the metals is mainly surface complexation. This research further reveals the dynamic response of its structural components when GRSP sequestrates heavy metals in mangrove sediment and aqueous ecosystems, demonstrating a new perspective for the transport and transformation of heavy metals onto GRSP.