In this study, we evaluated the long-term surgical outcomes of lensectomy-vitrectomy with primary intraocular lens (IOL) implantation in children with bilateral congenital cataracts (CCs) and investigated the potential risk factors for low vision. A total of 148 eyes in 74 children who underwent lensectomy-vitrectomy with primary IOL implantation were enrolled in this study. The surgery age was 44.04 ± 14.60 months, with a follow-up period of 46.66 ± 14.34 months. The final BCVA was 0.24 ± 0.32 logMAR, and low vision was found in 22 eyes (14.9%). Postoperative complications requiring additional surgeries included VAO (4 eyes, 5.4%), IOL pupillary captures (2 eyes, 2.0%), iris incarceration (1 eye, 0.7%), and glaucoma (1 eye, 0.7%). A higher incidence of VAO and larger postoperative refractive error was observed in younger children (≤2 years old) than in elder children (>2 years old) (p = 0.003, p = 0.047, respectively). Final BCVA was affected by preexisting comorbidity (p < 0.001), cataract density (p < 0.001), cataract size (p = 0.020), occurrence of postoperative complications (p = 0.011), and ASE (p = 0.008). Multivariate analysis showed that denser cataracts (OR = 9.303, p = 0.035) and preexisting comorbidity (OR = 4.712, p = 0.004) were the significant predictors of low vision. In conclusion, lensectomy-vitrectomy with primary IOL implantation is an effective and safe treatment for CC. The long-term visual outcome is encouraging in children with bilateral CC undergoing this procedure with a low rate of postoperative complications requiring surgeries. Moreover, eyes with denser cataracts and preexisting comorbidity may have a high risk of low vision.