Abstract Background Compared to conventional intensity‐modulated photon radiation therapy (IMRT), intensity‐modulated proton radiation therapy (IMPT) has potential to reduce irradiation‐induced late toxicities while maintaining excellent tumor control in patients with nasopharyngeal carcinoma (NPC). However, the relevant cost‐effectiveness remains controversial. Methods A Markov decision tree analysis was performed under the assumption that IMPT offered normal tissue complication probability reduction (NTCP reduction) in long‐term dysphagia, xerostomia, and hearing loss, compared to IMRT. Base‐case evaluation was performed on T2N2M0 NPC of median age (43 years old). A Chinese societal willingness‐to‐pay threshold (33558 US dollars [$])/quality‐adjusted life‐year [QALY]) was adopted. Results For patients at median age and having NTCP reduction of 10%, 20%, 30%, 40%, 50%, and 60%, their incremental cost‐effectiveness ratios were $102684.0/QALY, $43161.2/QALY, $24134.7/QALY, $13991.6/QALY, $8259.8/QALY, and $4436.1/QALY, respectively; IMPT should provide an NTCP reduction of ≥24% to be considered cost‐effective. Conclusions IMPT has potential to be cost‐effective for average Chinese NPC patients and should be validated clinically.