To investigate the postoperative clinical outcomes and axial length (AL) growth of infants with congenital cataracts and microphthalmos following first-stage cataract surgery. Retrospective case-control study. Setting: Single centre. Infants with congenital cataract that met the inclusion criteria were classified into two groups: the microphthalmos and comparison groups. All infants underwent a thorough ophthalmologic examination before surgery, and one week, 1 month, 3 months, and every 3 months after surgery. This study enrolled 21 infants (42 eyes) in the microphthalmos group and 29 infants (58 eyes) in the comparison group. More glaucoma-related adverse events were observed in the microphthalmos group (7 eyes, 16.7%) than in the comparison group (0 eyes, 0%) (p < 0.001). At each subsequent follow-up, the comparison group had a greater AL than the microphthalmos group (all p < 0.001), and AL growth was significantly higher in the comparison group than in the microphthalmos group (all p = 0.035). Visual acuity improvement in the microphthalmos group was similar to that of the comparison group. Early surgical intervention improves visual function in infants with congenital cataracts and microphthalmos although with a higher incidence of glaucoma-related adverse events. After cataract removal, the AL growth of microphthalmic eyes is slower than that of normally developed eyes.