The present study aims to explore the correlation of human leucocyte antigen (HLA)-DQ and tumour necrosis factor (TNF)- alpha gene polymorphisms with ocular myasthenia gravis (OMG) combined with thyroid-associated ophthalmopathy (TAO). From March 2009 to March 2015, 56 OMG patients complicated with TAO (OMG + TAO group), 134 patients diagnosed with OMG only (OMG group) and 236 healthy individuals (control group) were enrolled in the present study. PCR- sequence specific primer (PCR- SSP) was used for HLA- DQ genotyping and PCR- restriction fragment length polymorphism (PCR- RFLP) for TNF-alpha genotyping. ELISA kit was applied to detect acetylcholine receptor antibody (AchRAb) level and chemiluminescence immunoassay (CLIA) to measure thyroid- associated antibody (T- Ab) level. Logistic regression analysis was carried out to analyse the risk factors for OMG combined with TAO. DQA1*0103 showed lower frequency in the OMG group than in the control group. DQA1*0301 showed increased and DQB1*0601 showed decreased frequency in the OMG + TAO group. DQB1*0501 showed higher frequency in the OMG and OMG + TAO groups than in the control group. Patients carrying TNF-alpha - 863C > A (CA + AA) might confront with greater risks of OMG combined with TAO. Frequency of DQA1*0103/*0301 and DQB1*0501/*0601, and TNF-alpha- 863C > A, - 238G > A and - 308G > A were associated with the levels of AchRAb and T- Ab. TNF- alpha - 863C > A (CA + AA) and high level of T- Ab were risk factors for OMG combined with TAO. Our results demonstrate that TNF-alpha - 863 polymorphism is possibly correlated with the risk of OMG combined with TAO.