Orange peel was made into a highly efficient bio-sorbent by modification with cross-linking amine groups for perchlorate removal. Bench-scale experiments were performed to explore the factors affecting the perchlorate adsorption onto the modified orange peel (MOP). Perchlorate could be removed effectively at a wide range of pH (from 1.5 to 11). The maximum adsorption capacity of MOP for perchlorate was calculated as 154.1 mg/g within 15 min. The Redlich–Peterson model was fitted to the adsorption isotherm very well (R2 > 0.99). The adsorption process was spontaneous and exothermic, which was proved by thermodynamic parameters (Gibbs energy and enthalpy). The pseudo-second-order kinetic model could provide satisfactory fitting of the experimental data (R2 > 0.99). The scanning electron microscopy and energy-dispersive X-ray analysis indicated that the surface of MOP became smooth and the contents of N and Cl in MOP were increased during the modification process. Elemental analysis results showed that the nitrogen content in MOP was increased to 5.5%, while it was 1.06% in orange peel. The adsorption mechanism was also explored using zeta potential and Fourier transform infrared spectroscopy analysis. Ion exchange was the primary mechanism responsible for uptake of perchlorate onto MOP.