In this work we developed a one-step process for synthesizing carboxylic-functionalized carbon nanofibers (CNFs)-encapsulated Ni magnetic nanoparticles (Ni@CNFs) that exhibit an excellent magnetic response and a large content of hydrophilic carboxylate groups with a negative charge (RCOO(-)) on the carbon surface. The carbon-encapsulated magnetic Ni nanoparticles could be rapidly separated from water, and they showed high efficiency for adsorption of the antibiotic sulfamethoxazole (SMX) in aqueous solution. The adsorption of SMX on Ni@CNFs as a function of pH was investigated, and the greatest adsorption occurred at pH 7.0. The adsorption isotherms for SMX on Ni@CNFs depended on different pH values. A Monte Carlo simulation was used to probe the relationship between molecular conformation and π-π interaction. The high adsorption of SMX on Ni@CNFs at pH 7.0 could be ascribed to deprotonated SMX being easily converted to a planar-like conformation, thereby resulting in the formation of π rings that were approximately parallel to the graphite surface and that enhanced strong π-π interaction. Electrostatic and π-π interactions both contributed to deprotonated SMX adsorption at pH 7.0, and they influenced the adsorption isotherm toward the Freundlich model. However, in weakly acidic environments (pH 2.0 and 4.0), the electrostatic interaction alone could induce an adsorption pattern that was similar to the Langmuir model.