Background:We aimed to propose a deep learning-based approach to automatically measure eyelid morphology in patients with thyroid-associated ophthalmopathy (TAO).Methods: This prospective study consecutively included 74 eyes of patients with TAO and 74 eyes of healthy volunteers visiting the ophthalmology department in a tertiary A hospital. Patients diagnosed as TAO and healthy volunteers who were age-and gender-matched met the eligibility criteria for recruitment.Facial images were taken under the same light conditions. Comprehensive eyelid morphological parameters, such as palpebral fissure (PF) length, margin reflex distance (MRD), eyelid retraction distance, eyelid length, scleral area, and mid-pupil lid distance (MPLD), were automatically calculated using our deep learningbased analysis system. MRD1 and 2 were manually measured. Bland-Altman plots and intraclass correlation coefficients (ICCs) were performed to assess the agreement between automatic and manual measurements of MRDs. The asymmetry of the eyelid contour was analyzed using the temporal: nasal ratio of the MPLD. All eyelid features were compared between TAO eyes and control eyes using the independent samples t-test.Results: A strong agreement between automatic and manual measurement was indicated. Biases of MRDs in TAO eyes and control eyes ranged from −0.01 mm [95% limits of agreement (LoA): −0.64 to 0.63 mm] to 0.09 mm (LoA: −0.46 to 0.63 mm). ICCs ranged from 0.932 to 0.980 (P<0.001). Eyelid features were significantly different in TAO eyes and control eyes, including MRD1 (4.82±1.59 vs.2.99±0.81 mm; P<0.001), MRD2 (5.89±1.16 vs. 5.47±0.73 mm; P=0.009), upper eyelid length (UEL) (27.73±4.49 vs. 25.42±4.35 mm; P=0.002), lower eyelid length (LEL) (31.51±4.59 vs. 26.34±4.72 mm; P<0.001), and total scleral area (SA TOTAL ) (96.14±34.38 vs. 56.91±14.97 mm 2 ; P<0.001). The MPLDs at all angles showed significant differences in the 2 groups of eyes (P=0.008 at temporal 180°; P<0.001 at other angles). The greatest temporal-nasal asymmetry appeared at 75° apart from the midline in TAO eyes.Conclusions: Our proposed system allowed automatic, comprehensive, and objective measurement of eyelid morphology by only using facial images, which has potential application prospects in TAO. Future work with a large sample of patients that contains different TAO subsets is warranted.