To explore the application value of ultrasound and genetic testing in prenatal diagnosis and genetic counselling of fetal non-syndromic microphthalmia and anophthalmia. This paper reviewed 5 cases of isolated microphthalmia and anophthalmia by ultrasound, ultrasound imaging and subsequent genetic testing were followed up, to explore prenatal diagnosis and further genetic counselling for non-syndromic microphthalmia and anophthalmia. Five cases of microphthalmia/anophthalmia fetuses diagnosed by prenatal ultrasound. Case 1: 22 weeks of gestation, ultrasound shows anophthalmia of right eye, the fetus carried de novo pathogenic mutation of SOX2(p. Gly23Argfs*65). Case 2: 22 weeks of gestation with anophthalmia of both eyes, fetal carried de novo 3q26.33 deletion 1.92Mb, covering the pathogenic gene of SOX2. Case 3: 31 weeks of gestation, ultrasound shows microphthalmia of right eye, fetus carried a suspected de novo pathogenic mutation OTX2 c.448delA, associated with syndromic microphthalmia type 5. Case 4: 28 weeks of gestation, ultrasound showed bilateral microphthalmia, the fetus carried an vus mutation of LRP5, inherited from normal father. Case 5: 22 weeks' pregnant, ultrasound showed bilateral microphthalmia, and no mutation was detected. All pregnant women selected to terminate the pregnancy, and postnatal confirmed 100% of the ultrasound diagnosis. Anophthalmia and microphthalmia are the most serious developmental eye abnormalities, non-syndromic microphthalmia and anophthalmia are closely related to gene mutations, and prenatal ultrasound screening can reduce neonatal eye blindness, and apply more accurate genetic counselling on the results of genetic testing. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.