Selenium (Se) and chromium (Cr) in water might be harmful because of their high toxicity in the aquatic environment. Efficient removal of their hexavalent forms (Se(VI) and Cr(VI)) from extreme acidic wastewater is still challenging. Therefore, several new hydrochars suited for efficient removal of trace Se(VI) and Cr(VI) from acidic wastewater were fabricated from biomass through a hydrothermal method. Most functional groups were retained in the hydrochar, which gave it an excellent adsorption capacity (43.2 mg·g−1 and 132 mg·g−1 for Se(VI) and Cr(VI), respectively). After one batch treatment at exceptionally low pH and a hydrochar dose of 0.2 g·L−1, Se(VI) and Cr(VI) could be removed from 1 mg·L−1 to 6 μg·L−1 and 15 μg·L−1, respectively. The mechanism of adsorption at various pH was elucidated by Scanning Electron Microscopy, Thermogravimetry, Fourier Transform Infrared Spectrometer, X-Ray Photoelectron Spectroscopy and density functional theory (DFT) calculation. The adsorption mechanism for Se(VI) in acidic solution involved the binding of SeO42− with protonated amino groups (−NH3+) of Mix hydrochar. In the pH range of 6.5 to 7, Cr(VI) combined with −NH3+ functional groups primarily in the form of CrO42−. When the pH fell below 6.5, Cr(VI) bound with both −NH3+ and carbonyl groups (−C=O) in the form of HCrO4−. Fast kinetics were observed during the removal process of Se(VI) and Cr(VI). The hydrochar adsorbent showed good stability under acidic environments and during long-term adsorption cycles. These findings may provide theoretical basis for design of adsorption materials for acidic wastewater treatment.