We wanted to investigate the quantitative characteristics of humeral head migration (HHM) in shoulder osteoarthritis (OA) and their possible associations with scapular morphology. We quantified CT-scan-based-HHM in 122 patients with a combination of automated 3D scapulohumeral migration (=HHM with respect to the scapula) and glenohumeral migration (=HHM with respect to the glenoid) measurements. We divided OA patients in Group 1 (without HHM), Group 2a (anterior HHM) and Group 2b (posterior HHM). We reconstructed and measured the prearthropathy scapular anatomy with a statistical shape model technique. HHM primarily occurs in the axial plane in shoulder OA. We found “not-perfect” correlation between subluxation distance AP and scapulohumeral migration values (rs = 0.8, p < 0.001). Group 2b patients had a more expressed prearthropathy glenoid retroversion (13° vs. 7°, p < 0.001) and posterior glenoid translation (4 mm vs. 6 mm, p = 0.003) in comparison to Group 1. Binary logistic regression analysis indicated prearthropathy glenoid version as a significant predictor of HHM (χ² = 27, p < 0.001). Multivariate regression analysis showed that the pathologic version could explain 56% of subluxation distance-AP variance and 75% of the scapulohumeral migration variance (all p < 0.001). Herewith, every degree increase in pathologic glenoid retroversion was associated with an increase of 1% subluxation distance-AP, and scapulohumeral migration. The occurrence of posterior HHM is associated with prearthropathy glenoid retroversion and more posterior glenoid translation. The reported regression values of HHM in the function of the pathologic glenoid version could form a basis toward a more patient-specific correction of HHM.