Purpose:To quantitatively analyze the effect of TomoTherapy MVCT different scan options on IGRT(Image Guided Radiotherapy)and ART(Adaptive Radiotherapy)accuracy.Materials and Methods:The CT simulator images of CIRS-002LFC chest phantom and CIRS-002PRA pelvic phantom were scanned and transferred to TomoTherapy TPS.The spine and soft tissue were contoured as virtual whole spine and prostate cancer irradiation plans on each CT sets respectively.There options of Acquisition Pitch(fine,normal,coarse)and the corresponding two options of Reconstruction Interval for each Acquisition Pitch(fine:1mm or 2mm,normal:2mm or 4mm,coarse:3mm or 6mm)were used respectively to scan the chest and pelvic phantoms on Tomo couch.And after that,the couch with phantom was shifted 5mm to X,Y,Z positive directions respectively.MVCT scan with six different options were repeated for both phantoms.The first set of MVCT images(without shift)were used to investigate dosimetry effects on 'Tomo Planned Adaptive' module.The second set of MVCT images(with shift)were used to investigate the registration accuracy effects.DTA()was used to evaluate the registration errors where x,y,z stands for the registration errors on each(x:lateral,y:longitude,z:vertical)directions.Finally,the Tomo cheese phantom was scanned with three Acquisition Pitch options and the MVCT images were analyzed on noise and CT values.Results:For MVCT image sets of cheese phantom,there's no significant difference from different Acquisition Pitch options on image noise and CT values(shown in Fig.1).For MVCT image sets of chest and pelvic phantoms,there's no significant difference from different Acquisition Pitch and Reconstruction Interval options on adaptive dose calculation(shown in Fig.2).From the chest phantom,the bigger registration errors(DTA≥2mm)came from normal-4mm,coarse-3mm and coarse-6mm options and appeared mainly in longitude direction.From the pelvic phantom,the bigger registration errors came from coarse-3mm and coarse-6mm options and appeared mainly in longitude direction too.With the same Acquisition Pitch and Reconstruction Interval options,the 'Bone and Tissue Technique' registration option gave bigger errors while 'Full Image Technique' gave the smallest errors.Conclusions:The different scan options will not affect the dose calculation accuracy on MVCT.Therefore,the faster scan mode(coarse+6mm)is recommended for ART plan evaluation.While in position correction of IGRT,normal+2mm option is recommended and the 'Full Image Technique' may improve the registration accuracy.Manual registration correction is necessary after automatic registrations.