The ocular biometry characteristics are clinically significant for children with unilateral congenital cataracts, but there is a lack of data analysis concerning the preoperative measurements. The axial length (AL), mean keratometry (Km), corneal astigmatism (CA), and the anterior chamber depth (ACD) from both eyes before cataract surgery were obtained from 205 patients (410 eyes, 3-15 years of age) with unilateral congenital cataracts. In the congenital cataract eyes, shorter AL (22.44 ± 1.52 mm vs. 22.57 ± 1.04 mm, p = 0.036) and higher CA (- 1.89 ± 0.91 D vs. - 1.24 ± 0.67 D, p < 0.001) were found, and no significant difference was found in the Km and the ACD measurements compared to the contralateral normal eyes. Females had shorter AL and shallower ACD compared to males. However, the Km and CA in the females were significantly larger than that in males. Shorter AL, larger Km, higher CA, and shallower ACD were also found in females who had a binocular axial difference (the value obtained by subtraction of the contralateral normal eye from the congenital cataract eye) that less than zero. The preoperative ocular biometry of shorter AL, larger Km, higher CA, and shallower ACD should be considered in females with unilateral congenital cataracts. The age and the binocular axial differences had a statistically significant correlation (r = -0.192, p = 0.006). Therefore, changes in the binocular axial differences associated with aging may enhance the guidelines for intraocular lens selection and the management of congenital cataracts.