Background and purpose Online adaptive correction in image-guided intensity-modulated radiotherapy appeared to be a promising approach for precision radiation treatment in head and neck tumors. This protocol was designed to evaluate the clinical feasibility and effect of online cone beam computed tomography (CBCT) guidance in IMRT of nasopharyngeal cancer (NPC). Methods and materials The Elekta Synergy system, which integrates an X-ray volumetric imager (XVI), was used to deliver radiation treatment for 22 cases of NPC. The acquired CBCT was registered to the planning CT for online and offline analysis. The systematic and random setup errors, as well as planning target volume (PTV) margin, were calculated at different correction threshold levels. The impact of online setup correction on dosimetry was evaluated by simulation of pre-correction errors. Results The correction-of-setup-errors frequencies for 1, 2 and 3 mm thresholds were 41.3–53.9%, 12.7–21.2% and 6.3–10.3%, respectively. Online correction was effective at the 2 mm threshold level for all three axes. The pre-correction systematic errors for the whole group ranged 1.1–1.3 mm, and the random errors were also 1.1–1.3 mm. After online correction, the systematic and random errors ranged 0.4–0.5 mm and 0.7–0.8 mm, respectively, in the three directions. The PTV margins for the pre-correction, pretreatment and post-treatment positions were 3.5–4.2 mm, 1.6–1.8 mm and 2.5–3.2 mm, respectively, in three directions. Analysis of hypothetical dosimetric change due to a translational isocenter shift of 3 mm showed that if no correction was applied, the mean maximum dose to both the brain stem and spinal cord would be increased by 10 Gy, the mean dose to the left and right parotids would be increased by 7.8 and 8.5 Gy, respectively, and the dose to target volumes would be decreased: 4 Gy for 95% GTV and 5.6 Gy for 95% CTV 60. Conclusions CBCT-based online correction increased the accuracy of IMRT for NPC and reduced irradiated margins, by decreasing both the systematic and random errors. Online CBCT correction reduces the radiation dose to normal tissue and creates room for further dose escalation of tumors.