Background: Etiologies of congenital microphthalmia and anophthalmia are unclear and commonly thought to be homogenous. To test if risk factors are similar for these two diseases, we compared the risk factors between congenital microphthalmia and anophthalmia in a large Chinese cohort. Methods: A total of 347 patients with congenital microphthalmia or anophthalmia diagnosed by magnetic resonance imaging (MRI), computed tomography (CT) or ultrasound from 2011 to 2018 were enrolled. Patients' clinical information, used as potential risk factors, was retrospectively collected. A multivariable logistic regression model was used to estimate odds ratios (OR) and 95% confidence intervals (CI). Results: A total of 347 patients were affected by congenital microphthalmia or anophthalmia. A total of 324 cases were microphthalmia, and 23 cases were anophthalmia. Structural abnormalities, mother's age at initial pregnancy, whether the mother drinks, whether the mother was diseased during pregnancy and whether the father has systemic disease passed the univariate test. In the multivariable logistic regression model, whether the mother was diseased during pregnancy (OR=2.804, P=0.023) and whether the father had systemic disease (OR=4.795, P=0.027) are significant risk factors for anophthalmia over microphthalmia. Influenza or common cold infection accounted most of the mother's diseases during pregnancy. Conclusions: Mothers with diseases, mainly influenza or common cold infection, during pregnancy are more likely to have baby with anophthalmia than microphthalmia. Our study indicated that there might be different etiologies for anophthalmia and microphthalmia.