Abstract Background Axenfeld-Rieger syndrome (ARS) is a congenital disease with a series of developmental abnormalities, and no case of ARS with cataract and small cornea has been reported in previous studies. In the present report, we aimed to describe the diagnosis and phacoemulsification of an ARS patient with small cornea. Case presentation A 58-year-old Han Chinese male patient who was referred to Eye Center of the Second Affiliated Hospital of Zhejiang University Medical College was diagnosed with ARS. Systemic and ophthalmic examination and genetic testing were performed. The slit-lamp microscopic examination of anterior segment showed obvious nuclear cataract, iris lesions, and the abnormal cornea of both eyes with small transversal and longitudinal diameters. ARS with bilateral complicated cataract and small cornea was diagnosed. Microincision-phacoemulsification in combination with intraocular lens implantation was performed on his left eye. After successful surgery of his left eye, the best-corrected visual acuity (BCVA) was obviously improved from 2 to 0.5 (LogMAR). A transient elevation of intraocular pressure (IOP) was controlled with medication. Conclusions Through genetic testing, a known pathogenic mutation NM_153427.2:c.272G > A was detected on the PITX2 gene; and an unknown mutation NM_001453.2:c.1063C > T was detected on FOXC1 gene. For the ARS patient with complicated cataract, the visual acuity was increased by phacoemulsificasion in combination with microincision.