Herein, we proposed a novel chitosan-induced self-assembly strategy to construct three-dimensional magnetic MXenes/chitosan composites to eliminate U(VI)/Cr(VI). Spectroscopic analysis elucidated that the magnetic composites exhibited a three-dimensional network structure, and the abundant –OH and –NH2 groups played a pivotal role in boosting elimination performance of the composites. Batch experiment demonstrated that the synergistic effect of the amino and hydroxyl groups contributed greatly to adsorption, and the maximum adsorption capacity of U(VI) and Cr(VI) was up to 106.2 and 83.1 mg/g, respectively. Meanwhile, the kinetic studies showed that an obvious transition between diffusion control and mass transfer control, and the adsorption behavior was endothermic and spontaneous. Furthermore, a comprehensive synergistic adsorption mechanism was proposed based on the systematic spectra analysis. Namely, the target contaminant was rapidly immobilized on the 3D composites via electrostatic interaction, then the U(VI) was complexed with the amino groups, while a part of Cr(VI) was reduced to Cr(III) by the hydroxyl groups. Thus, this study not only paved the way for mitigating the increasing heavy metal/radionuclide contamination, but also promoted the application of MXexes-based materials in the field of environmental remediation.