Background To analyze the relationship between the rotational and residual setup errors and the dose deviation on nasopharyngeal carcinoma (NPC) treated by helical tomotherapy (HT). Methods From 25 July 2017 to 20 August 2019, 16 treated NPC patients were enrolled in the study. These patients were scanned with full target range megavoltage computed tomography (MVCT) every other day. Adaptive radiotherapy function application software MIM7.1.3 were used to accumulate the actual dose. The dose deviation with the initial plan dose of the patients’ target and organs at risk (OAR) were compared, and the correlation between the dose change and the setup errors (rotational setup errors and neck residual setup error) was analyzed. Results Translational setup errors increased farther away from the head. Statistically significant difference among 3 groups was achieved in the directions of left-right ( P < .001) and anteroposterior ( P < .001) by analysis of variance test. Compared with the initial plan dose, the actual accumulated dose of the target area decreased with the actual exposure dose of the OAR increased. However, most of the dosimetric parameters differed by less than 5%. No correlation was found between dose deviation values and the translational setup errors of target. However, sagittal rotational setup errors (pitch) had a positive relationship ( P < .05) with the avearge dose of PTVnd (L) ( r = 0.885), PTVnd(R) ( r = 0.547) PTV1( r = 0.633) and PTV2( r = 0.584). Transverse rotational setup errors (roll) had a positive relationship ( P < .05) with the avearge dose of PTVnd(R) ( r = 0.593), PTV1( r = 0.505) and PTV2( r = 0.662). Conclusions Dose deviation between the actual accumulated and initial plan is not negligible, but most indicators difference is less than 5%, NPC patients treated by HT with MVCT correction setup errors every other day did not need adaptive radiotherapy model unless got rapid tumor shrinkage or weight loss. Moreover, to minimize the dose deviation, more attention should be paid to the reduction of pitch, roll, and residual error of cervical vertebrae during body positioning.