Developing high-efficient capacitive deionization (CDI) systems with low-cost environmentally friendly electrode materials is one of the most effective ways to address freshwater shortage. Meanwhile, large number of soybean roots are discarded as waste with large production of soybean and contribute to enormous pressure on the environment. In this work, soybean roots are adopted to prepare activate carbon (SRKPC) by a carbonization and KOH activation process. A composite of [email protected]2 with MnO2 nanoparticles supported on SRKPC is synthesized by a low temperature hydrothermal reaction, which exhibits excellent electrochemical properties with high specific capacitance (597.9 F g−1 at 2 mV s−1) and bimode sodium storage characteristics. The dual-mode CDI system based on [email protected]2 delivers an effective desalination performance with a desalination capacity of 42.90 mg g−1, a desalination rate of 2.86 mg g−1 min−1 and relatively good desalination recoverability. Therefore, this work not only exemplifies the simple fabrication of low-cost, environmentally friendly, and efficient dual-mode CDI electrode materials for capacitive desalination, but also provides a sustainable way to turn biomass waste into functional materials.