Background: This study aimed to present the genetic profile of a rare ocular disease nanophthalmos (NO) in a large Chinese cohort, to explore its genetic characteristics and genotype-phenotype correlations. Methods: A total of 43 unrelated pedigrees diagnosed with NO were recruited. Whole exome sequencing and copy number variation analysis were performed, followed by validation and pathogenicity classification of the detected variants. Results: The overall genetic diagnostic rate was 60.5%. Twenty-eight unique genetic variants of MFRP, PRSS56, and MYRF have been identified, of which 19 were reported for the first time. The c.1486G>A variant in MFRP and the c.1066dupC variant in PRSS56 were the two most frequent variants. Patients with variants in MFRP or PRSS56 tended to possess shorter axial lengths than those with MYRF variants. Among patients with MFRP null variants, a higher proportion developed uveal effusion syndrome (UES) than did those without null variants, whereas among patients with PRSS56 null variants, a greater number of patients developed angle-closure glaucoma (ACG). A higher proportion of MFRP-related NO patients developed both UES and ACG. Conclusions: MFRP, PRSS56, and MYRF account for the majority of genetic causes of NO. MFRP-related NO patients tend to exhibit a strong predisposition to complications. Null variants in MFRP and PRSS56 may increase susceptibility to clinical complications. This study provides insights into the genetic landscape and clinical characteristics of NO. These findings will lead to a better understanding of the mechanisms underlying nanophthalmos and other diseases associated with eye development.