Developing suitable and efficient adsorbents to remove organic dyes from wastewater become a hot topic. Herein, core-shell sp3@sp2 nanocarbons (ND-700, ND-900, ND-1100 and ND-1300), consisting of diamond core and graphitic shell with variable sp2/sp3-carbon ratio, were prepared by annealing nanodiamonds (NDs) at various temperatures (700–1300 °C). The increased graphitization degree of the nanocarbons with the increase of annealing temperature was confirmed by X-ray diffraction (XRD) and high-resolution Transmission Electron Microscopy (HRTEM). Sequentially, these nanocarbons were utilized as solid adsorbents to remove anionic methylene orange (MO) and cationic methylene blue (MB). Results show that although all of the nanocarbons are positively charged, the nanocarbons with higher graphitization (ND-1100, ND-1300) exhibit higher adsorption performance for both MB and MO. This can be attributed to the forming of π-π interaction between the graphitic surface and aromatic rings within the dye molecules. The ND-700 exhibits little adsorption for cationic MB for its low graphitization as well as electrostatic repulsion. The adsorption of MO and MB on ND-700 and ND-1300 in the binary MO/MB system was also investigated, respectively. Results show that the ND-1300 could adsorb MO and MB efficiently and simultaneously, and ND-700 exhibits selective adsorption for MO from the binary system.