To compare the refractive outcome and postoperative complications of cataract surgery among nanophthalmos and relative anterior microphthalmos and the normal control eyes. Retrospective case-control series. Seventeen eyes with nanophthalmos, 29 eyes with relative anterior microphthalmos, and 54 normal control eyes were enrolled in this study. The subjects were divided into 3 diagnostic subgroups according to the following: nanophthalmos with an axial length <20.5 mm and without morphologic malformation; relative anterior microphthalmos with a corneal diameter (CD) ≤ 11 mm, an anterior chamber depth (ACD) ≤ 2.2 mm, and an axial length (AL) ≥ 20.5 mm; and normal control group eyes defined as an AL ≥ 20.5 mm with a CD >11 mm or an ACD >2.2 mm. The implanted intraocular lens (IOL) power was used to calculate the predicted postoperative refraction error according to 4 IOL power formulas: SRK II, SRK/T, Hoffer Q, and Holladay 1. With each formula, the mean numeric error and mean absolute error were calculated. At postoperative 2 months, the endothelial cell count and the complications were analyzed. As measured by mean numeric error or mean absolute error, there was a significant difference among the 3 groups based on SRK II, SRK/T, and Hoffer Q, with less predictability in the nanophthalmic eyes. In eyes with nanophthalmos, the Holladay 1 produced the best refractive results as measured by mean numeric error (P < .001). A higher occurrence rate of posterior capsule rupture (11.7%) was shown in the nanophthalmic eyes. The difference among the 3 groups for the postoperative endothelial cell loss was not significant (P = .421). The refractive predictability and postoperative outcome was poorer in the eyes with nanophthalmos compared to the eyes with relative anterior microphthalmos or normal control.