To verify the feasibility of our in-house developed multi-sequence magnetic resonance (MR)-generated synthetic computed tomography (sCT) for the accurate dose calculation and fractional positioning for head and neck MR-only radiation therapy (RT).Forty-five patients with nasopharyngeal carcinoma were retrospectively studied. By applying our previously in-house developed network, a patient's sCT can rapidly be generated with respect to feeding the sole T1 image, T1C image, T1DixonC image, T2 image, and their combination respectively (five pipelines in total). A k(5)-fold strategy was implemented during model establishment. Dose recalculation was performed for each pipeline generation to attain a dosimetric feasibility evaluation. Fractional positioning evaluation was performed by calculating the digitally reconstructed radiograph (DRR) of the sCT and planning CT and their offset to the portal image.The dose mean absolute error values are (0.47±0.16)%, (0.48±0.15)% (p<0.05), (0.50±0.16)% (p<0.05), (0.50±0.15)% (p<0.05), and (0.45±0.16)% (p<0.05) for the T1, T1C, T1Dixon C, T2, and 4-channel generated sCT to the prescription dose, respectively. The 4-channel-generated sCT outperforms any other single-sequence pipelines. Among the single-sequence MR imaging-generated sCTs, the T1-generated shows the most accurate HU image quality and provide a reliable dose result. Quantified positioning errors with calculation of the difference to the planning CT offsets are (-0.26±0.50)mm, (-0.58±0.52)mm (p<0.05), (-0.27±0.57)mm (p>0.05), (-0.31±0.44)mm (p>0.05), and (-0.19±0.37)mm (p>0.05) at LNG and (0.34±0.53)mm, (0.48±0.56)mm (p>0.05), (0.55±0.56)mm (p>0.05), (0.37±0.61)mm (p>0.05), and (0.24±0.43)mm (p>0.05) at LAT of the anterior-posterior direction for the five pipelines.Multi-sequence MR-generated sCT allows for accurate dose calculation and fractional positioning for head and neck MR-only RT. This article is protected by copyright. All rights reserved.This article is protected by copyright. All rights reserved.