Novel pectin derived from sweet potato residue was modified by high hydrostatic pressure (HHP)-assisted pectinase and then used for Pb2+ removal from aqueous solutions. The removal characteristics and mechanisms were also investigated. Results showed that modified sweet potato pectin exhibited greater adsorption performances for Pb2+ than that of natural ones, and showed excellent eco-friendly properties and good potential for adsorption of some other heavy metals (such as Cu2+). The adsorption curves were much more conformed to Langmuir model, and the highest capacity for Pb2+ adsorption was 263.15 mg/g with 1.00% pectin at pH 7. Chemical adsorption process of pectin for Pb2+ absorption involved O-containing functional groups (O–H, COO-), cation exchange, and along with electrostatic interactions. Overall, the results in this study indicated that sweet potato pectin modified with HHP-assisted pectinase had the potential to become an environmentally friendly coagulant-flocculant agent for the heavy metal adsorption, especially for Pb2+.