Carbon doped Fe3O4 nanoparticles (Fe3O4/C) prepared by a facile hydrothermal reaction of glucose with iron resource have been applied as magnetic solid-phase extraction (MSPE) sorbent, for the first time, to extract trace brominated flame retardants (BFRs) and pentachlorophenol (PCP) from environmental waters. Various MSPE parameters were optimized including amount of Fe3O4/C nanoparticles, pH of sample solution, enrichment factor of analytes and reusability of Fe3O4/C sorbent. The reliability of the MSPE method was evaluated by the recoveries of BFRs and PCP in spiked water samples. Good recoveries (80.0–110.0%) were achieved with the relative standard deviations range from 0.3% to 6.8%. In this paper, the extraction characteristics of Fe3O4/C sorbent were further elucidated. It is found that the adsorption process of Fe3O4/C to analytes predominates the MSPE efficiency. There is hybrid hydrophobic interaction and hydrogen bonding or dipole–dipole attraction between Fe3O4/C and analytes. Notably, the chemical components of carbon layer on the surface of Fe3O4 nanoparticles were identified by X-ray photoelectron spectroscopy and thermogravimetry-mass spectrometry, and in consequence the covalent bonds between Fe3O4 and the coated carbon have been observed. In addition, the straight influence of synthesis condition of Fe3O4/C nanoparticles including glucose concentration and hydrothermal reaction time on extraction performance for BFRs and PCP has been investigated. It is confirmed that the existence of organic carbon containing functional groups over Fe3O4/C sorbent is responsible for the MSPE extraction.