Whole-body dynamic fluoro-D-glucose (FDG)-positron emission tomography (PET) imaging through continuous-bed-motion (CBM) mode multi-pass acquisition protocol is a promising metabolism measurement. However, inter-pass misalignment originating from body movement could degrade parametric quantification. We aim to apply a non-rigid registration method for inter-pass motion correction in whole-body dynamic PET. 27 subjects underwent a 90-min whole-body FDG CBM PET scan on a Biograph mCT (Siemens Healthineers), acquiring 9 over-the-heart single-bed passes and subsequently 19 CBM passes (frames). The inter-pass motion correction was executed using non-rigid image registration with multi-resolution, B-spline free-form deformations. The parametric images were then generated by Patlak analysis. The overlaid Patlak slope and y-intercept images were visualized to qualitatively evaluate motion impact and correction effect. The normalized weighted mean-squared Patlak fitting errors (NFEs) were compared in the whole body, head, and hypermetabolic regions of interest (ROIs). In images, ROI statistics were collected and malignancy discrimination capacity was estimated by the area under the receiver operating characteristic curve (AUC). After the inter-pass motion correction was applied, the spatial misalignment appearance between and images was successfully reduced. Voxel-wise normalized fitting error maps showed global error reduction after motion correction. The NFE in the whole body ( 0.0013), head ( 0.0021), and ROIs ( 0.0377) significantly decreased. The visual performance of each hypermetabolic ROI in images was enhanced, while 3.59% and 3.67% average absolute percentage changes were observed in mean and maximum values, respectively, across all evaluated ROIs. The estimated mean values had substantial changes with motion correction ( 0.0021). The AUC of both mean and maximum after motion correction increased, possibly suggesting the potential of enhancing oncological discrimination capacity through inter-pass motion correction.