Rotator cuff tear arthropathy (RCTA) is characterized by massive rotator cuff tearing combined with humeral head migration (HHM). The aim of this study is to investigate the quantitative characteristics of this migration and its association with glenoid erosions and prearthropathy scapular anatomy. We quantified HHM and prearthropathy scapular anatomy of 64 RCTA patients with statistical shape modeling-based techniques. Glenoid erosion was classified according to Sirveaux et al. A cutoff value for confirming HHM was 5 mm based on a control group of 49 patients. Group 1 (RCTA without HHM) consisted of 21 patients, with a mean subluxation distance (SLD) of 3 mm. Group 2 (RCTA with HHM) consisted of 43 patients, with mean SLD of 9 mm, SLD in the anteroposterior plane of −1 mm (SD ± 4 mm), SLD in the superoinferior plane of 7 mm (SD ± 3 mm), and subluxation angle (SLA) of −5° (SD ± 40°). Analysis with Fisher's exact test showed a clear association between HHM and glenoid erosions (p = 0.002). Multivariate regression analysis of Group 2 showed that prearthropathy lateral acromial angle combined with critical shoulder angle (p = 0.004) explained 21% of the observed variability in SLD. The prearthropathy glenoid version explained 23% of the variability in SLA (p = 0.001). HHM in RCTA patients has a wide variation in both magnitude and direction leading to a distorted glenohumeral relationship in the coronal and axial plane. HHM is highly associated with the occurrence of glenoid erosions. There is a correlation between the prearthropathy scapular anatomy and the magnitude and direction of HHM.