Serum proteins may be abnormally increased or decreased during the occurrence and development of nasopharyngeal carcinoma (NPC). However, currently there are no simple or effective methods to collect and differentiate these abnormally secreted proteins from abundant serum proteins. In this study, acetonitrile was used to remove the majority of high-abundance proteins from serum samples obtained from patients with NPC. The samples were subjected to surface-enhanced laser desorption/ionization time-of-flight mass spectrometry with a CM10 (weak cation exchange) ProteinChip, and the resulting protein profiles were compared with those of non-acetonitrile-treated serum samples. The results showed that the protein profiles differed between the acetonitrile- and non-acetonitrile-treated sera from patients with NPC. A large proportion of the non-acetonitrile-treated NPC serum protein peaks were <6000 kDa, while the detection rate of protein peaks >6000 kDa was relatively higher in the acetonitrile-treated NPC sera, accounting for more than half of all protein peaks (26.2+37.5%). Few differentially upregulated proteins were lost, and the peak value density increased after acetonitrile treatment. In conclusion, acetonitrile treatment of serum samples is effective in removing high-abundance macromolecular proteins. Therefore, acetonitrile treatment can be applied for the investigation of serum proteomics and may aid in the identification of differentially expressed proteins.