Two-dimensional (2D) layered materials for environmental remediation require abundant functional groups and high affinity for target pollutions. In this work, a heteroatom sulfur-doped graphitic carbon nitride (S3.9%-g-C3N4) material had been fabricated by pyrolysis for S- and N-rich supramolecular polymer precursor. A hierarchically porous structure with multimodal pore size distribution can facilitate Pb(II) ions’ diffusion from wastewater to the S3.9%-g-C3N4 surface. Batch adsorption experiments revealed that the resulting S-doped conjugated system of g-C3N4 exhibited enhanced adsorption capacity (52.63 mg g–1) as compared with that of individual g-C3N4 (31.25 mg g–1) at pH = 4.5. Accordingly, the higher adsorption ability for S3.9%-g-C3N4 was on account of its binding sites (i.e., soft S ligand) for coordination with Pb(II) than g-C3N4. Significantly, thermodynamic parameters demonstrated that the adsorption of Pb(II) on S3.9%-g-C3N4 was a spontaneous and endothermic process, and the kinetic experiments suggested that the chemisorption governed the adsorption process. Additionally, all geometries of (S-g-C3N4)–Pb(II) systems were thoughtfully constructed to explore the optimized structure, and these results were combined with the results of Density Functional Theory calculations to show that the enrichment of Pb(II) on S3.9%-g-C3N4 was energetically favored in C3N4–S–N3—the monosubstituted system with high Ead value (4.75 eV), in which the chemical binding sites of S–Pb and N–Pb were further evidenced by XPS analysis. The presented results not only demonstrated a facile and environmentally friendly strategy to synthesize porous S3.9%-g-C3N4 nanosheets with preferable Pb(II) adsorption ability, but also revealed the underlying adsorption mechanism for Pb(II) by experiments and theory simulation.