Magnetic mesoporous N-doped C (Fe3O4@N-mC) was obtained from the carbonization of mesoporous polyaniline Fe3O4@mPANI, which was fabricated by aniline directly polymerization around PVP-modified Fe3O4 particles. Surface modification and magnetic property were successfully introduced into the mesoporous C material with core-shell structure. Similar sizes of acidic methyl orange (MO), basic methyl blue (MB), and bulky-sized rhodamine B (RhB) were selected as target molecules to investigate the influences of molecular sizes and acidic-basic properties of the dyes on the adsorption behavior of Fe3O4@N-mC composite. Due to its spacious mesoporous structure and functional basic character, Fe3O4@N-mC composite displayed the adsorption ability in the order of MO > MB > RhB. The N-doped mesoporous C improved the adsorption to acidic dye compared with basic dye with the similar sizes. The adsorption kinetic was fitted with the pseudo-second-order model, suggesting that the chemical adsorption process was the rate-determining step for the whole adsorption process. The experimental adsorption capacities were well explained by the Langmuir model. Moreover, the introduced magnetic Fe3O4 made the composite easily separated from the solution after adsorption and regenerated with excellent stability. The fast and high adsorption performance, the easy separation, and excellent regeneration made Fe3O4@N-mC composite promising adsorbent candidate in practical wastewater treatment.