PURPOSE To study the effects of an individualized treatment approach to children with congenital microphthalmos and anophthalmos. METHODS Patients with congenital microphthalmos or anopthalmos with orbital cysts who were referred to Beijing Tongren Hospital between July 2009 and July 2017 were included in this retrospective case series study. For patients <= 6 years of age, the cyst was retained to promote orbital development unless a prosthesis could not be fitted at all or disproportionate orbital growth was detected. Hydrogel orbit expanders were implanted initially if orbital volume was poor. For patients >6 years of age, the cyst was removed if it caused cosmetic problems or unsatisfactory prosthesis fitting. Eyelid procedures were performed after puberty to improve appearance. RESULTS The study included 26 orbits of 24 patients. Of the 14 patients <= 6 years, 3 underwent cyst excision, 8 were treated with conformers only, and 3 had hydrogel orbit expander implantation initially. Of the 10 patients >6 years, 1 had the cyst removed, 5 had eyelid surgeries without removing the cyst, 3 wore an artificial eye without any surgery, and 1 used no prosthesis. During the follow-up period (range, 6 months to 8 years), 23 patients had a good cosmetic outcome and were eventually able to retain an ocular prosthesis; 1 patient could not wear prostheses but refused further treatment. No procedure-related complications were noted. CONCLUSIONS The individualized treatment of congenital microphthalmos and anophthalmos with orbital cysts depends on the patient's age at presentation, the growth pattern of the cyst, and the volume of the affected orbit.