Considerable geometrical changes for the organs at risk (OARs) and target volumes occurred during concurrently/sequentially chemoradiotherapy (chemoIMRT) for nasopharyngeal carcinoma(NPC). This study aimed to qualify their longitudinal geometrical variations of the central nerve system related OARs(CNS-related OARs). The computed tomography (CT) images of 20 patients with locally advanced NPC were analyzed retrospectively. Each patient had planning CT (CTplan) with intravenous contrast and six weekly repeat CT (CTrepeat) without contrast. Each CTrepeat was rigidly registrated with bone match to its CTplan. The CNS-related OARs included spinal cord, brainstem, chiasm, optical nerves, eye globes, lens, and inner ear. In cranial-caudal direction, the cervical spinal cord was contoured at seven axial CT sections using seven radiological boundaries. The volume reduction, systematic (∑) and random (δ) errors in different directions, the 3-dimensional vector displacement, Dice similarity coefficiency (DSC), Overlapping index(OI), the shortest perpendicular distance (SPD) as their standardized deviation (SD) were calculated. The margin of CNS-related OARs was estimated with the margin recipe of 1.3∑+0.5σ. The volume loss of spinal cord, brainstem, and eye globes showed a linear decreasing time trend. with the mean of -6.5% ±4.8% (95% CI: -7.4%, -5.6%), -2.6%±2.3%(-3.0%, -2.1%), -9.5% ±7.4% (-10.4%, -8.6%) as radiation fraction elapsed. The volumetric reductions of spinal cord (R2=0.106, P=0.000) and brain stem (R2=0.378, P=0.000) were significantly correlated to weight loss. The mean DSC of spinal cord, brainstem, and eye globes were > 0.85 throughout the treatment. Both the mean SPD and its SD of spinal cord, brainstem, eye globes were < 1.2 mm during the treatment course. The OARs volume of chiasm, optical nerve, lens, and inner ear were < 1cm3. In addition, their volume changes varied from -15.4% to 2.6%, and DSC and OI were 0.47 - 0.80 and 0.33 - 0.69 respectively. The DSC of lens was < 0.6 throughout the treatment course. For all OARs, ∑ and δ were < 0.4mm and 1.7mm. The margin of OARs was < 3mm in left-right (LR), cranial-caudal (CC) and anterior-posterior (AP) direction. For the different axial levels of spinal cord, both the ∑ increased from the cranial to caudal direction and they were 0.13-0.70 mm and 0.12-0.64mm in LR and AP direction respectively, The δ did 0.40-1.52 mm and 0.4–1.42mm respectively. The recommended margins in different axial levels of spinal cord were 0.37-1.67 mm and 0.21-1.12 mm in LR and AP direction respectively. The volume, position, and shape of CNS-related OARs occurred considerable changes during the chemoIMRT course for NPC. The OARs with small volume occurred more shape variations and the position shifted differently in axial levels of spinal cord. The recommended margin was < 3mm as the individual OAR and its direction.