For the first time, C8-functionalized magnetic graphene (magG) has been designed and synthesized with a polydopamine (PDA) coating. The magG prepared by a solvothermal reaction was encapsulated in a layer of PDA through the oxidative polymerization of dopamine in alkaline buffer, and C8 groups were grafted onto magG/PDA composites through a silanization method. The as-prepared material integrates the merits of graphene, magnetic microspheres, PDA, and C8 chains; thus possessing an ultrahigh specific area, strong magnetic responsiveness, excellent solubility, and an extraordinary enrichment capability. The C8-functionalized magnetic composites were employed in the enrichment and identification of low-concentration standard peptides, peptides in standard protein digest solutions, and endogenous peptides in human urine. The enriched peptides were eluted and analyzed by MALDI-TOF MS. The MS results indicated that the C8-functionalized material exhibited the distinguished ability to enrich hydrophobic peptides mainly through hydrophobic–hydrophobic interactions. Moreover, thanks to the enrichment approach based on magG@PDA@C8, the limit of detection of the standard peptide decreased to as low as 50 pM. The experimental results demonstrate that the magG@PDA@C8 composite is a promising candidate for the enrichment of low-abundance peptides in biological samples.