Background: To evaluate microstructural changes in the meibomian glands (MGs) in patients with active and inactive Graves’ orbitopathy (GO), using in vivo confocal microscopy (IVCM), and to investigate the correlations between clinical and confocal findings.Methods: Forty patients (80 eyes) with GO (34 eyes with active GO, 46 eyes with inactive GO), and 31 age- and sex-matched control participants (62 eyes) were enrolled consecutively. Each participant completed an Ocular Surface Disease Index (OSDI) questionnaire and underwent a full eye examination, including assessments of clinical activity score (CAS), proptosis, palpebral fissure height (PFH), lagophthalmos, lipid layer thickness (LLT), partial blinking rate, noninvasive first breakup time (NIF-BUT), average breakup time (NIAvg-BUT), tear film breakup area (TBUA), corneal fluorescein staining (CFS), Schirmer I Test (SIT), meibum quality and MG expressibility. IVCM of the MGs was performed to determine the MG acinar density (MAD), MG longest and shortest diameters (MALD and MASD), MG orifice area (MOA), MG acinar irregularity (MAI), meibum secretion reflectivity (MSR), acinar wall inhomogeneity (AWI), acinar periglandular interstices inhomogeneity (API), and severity of MG fibrosis (MF).Results: All parameters demonstrated statistically significant differences among groups (all P<0.05), except OSDI, LLT and NIAvg-BUT (P>0.05). Compared to controls, GO groups showed lower MOA and MAD; greater MALD and MASD; and higher degrees of MAI, MSR, AWI, API, and MF (all P<0.05). Eyes with active GO had higher degrees of MAI, AWI, and API, while eyes with inactive GO had higher degrees of MSR and MF (all P<0.05). In GO groups, the two measured confocal signs of inflammation (AWI and API) were significantly correlated with CAS, proptosis, PFH, lagophthalmos, OSDI, NIF-BUT, CFS, SIT, meibum quality, and MG expressibility (all P<0.05). MF was significantly correlated with CAS, OSDI, meibum quality, and MG expressibility (all P<0.05). Conclusions: IVCM effectively revealed microstructural changes of MGs in eyes with GO and provided strong in vivo evidence for the roles of obstruction and inflammation in the ocular surface disease process. Furthermore, it revealed discernible patterns of MG abnormalities in eyes with active GO and inactive GO, which are not easily distinguishable by typical clinical examinations.