Medical exposure to ionizing irradiation has become a recognised carcinogenic risk. Balancing the concomitant imaging dose and positioning accuracy is critical in image-guided-radiotherapy (IGRT) especially for children, whose higher biological susceptibility and longer expected life make them more vulnerable to develop secondary cancer. This work aims to evaluate and benchmark the imaging dose and positioning accuracy of a new MV cone-beam-CT (CBCT)-guided IGRT system, Varian Halcyon, against conventional kV CBCT. Weighted-CT-dose-index (CTDIw) were measured for Varian TrueBeam kV CBCT, and computed for Halcyon MV CBCT using Eclipse system as validated before. Simulating the IGRT workflow, the positioning accuracy of correcting a known shift was tested on various regions of 1-year, 5-year and adult anthropomorphic phantoms, respectively. Inter-scanner and inter-protocol comparisons of dose and accuracy were performed. kV CTDIw for 'Head', 'Thorax', 'Pelvis' and 'Image Gently' (in CTDIΦ16cm/CTDIΦ32cm phantoms, respectively) protocols were measured as 4.5 mGy, 5.4 mGy, 19.3 mGy, and 1.1 mGy/0.5 mGy, respectively. Using 'High Quality' mode, MV CTDIw in the CTDIΦ16cm and CTDI Φ32cm phantoms were computed as 84.5 mGy and 63.8 mGy (imaging length = 28 cm), 68.8 mGy and 55.5 mGy (imaging length = 16 cm), respectively, which were about twice of 'Low Dose' mode. The maximum positioning deviation observed on Halcyon was 0.51 mm ('Low Dose' adult thorax), which was lower than that of standard (0.58 mm, 'Pelvis' adult pelvis) and 'Image Gently' kV CBCT (1.57 mm, adult pelvis). Accuracy of 'Image Gently' kV CBCT head & neck and thoracic imaging were clinically acceptable for adults (maximum deviation = 0.54 mm, adult thorax). Complying with Image Gently campaign, dose-efficient protocols should be used for pediatric IGRT, achieving comparable positioning accuracy on the new Halcyon MV CBCT system relative to the conventional kV CBCT.