<b><i>Introduction:</i></b> Data on the genetic landscape of congenital microcephaly (CM) in China are scarce, and the incidence of CM caused by the most commonly mutated gene <i>ASPM</i> in China remains unknown. <b><i>Methods:</i></b> Sixty-one neonates with CM who were hospitalized in the Children’s Hospital of Fudan University between August 1, 2016, and August 31, 2020, were enrolled, and the clinical data and clinical exome-sequencing data were analyzed. An additional 18,103 parental data entries from the Chinese Children’s Genetic Testing Clinical Collaboration System database were collected to estimate the incidence of <i>ASPM</i>-related congenital microcephaly (<i>ASPM</i>-CM) in East China by analyzing the carrier frequency of <i>ASPM</i> mutations. <b><i>Results:</i></b> Among the 61 neonates with CM, 35 (57.4%) patients were identified with genetic findings, including 24 patients with single nucleotide variants (SNVs) and 11 patients with copy number variations (CNVs). <i>ASPM</i> was the most common gene with detrimental SNVs detected in 3 patients. Patients with genetic findings showed a significantly higher incidence of developmental delay (91.3%, 21/23) than those without genetic findings (60%, 9/15) (<i>p</i> = 0.04). All the 3 decreased patients had genetic findings. The estimated <i>ASPM</i>-CM incidence in East China was 1/1,295,044. <b><i>Conclusion:</i></b> Comprehensive genetic testing, detecting both SNVs and CNVs, is recommended for newborns with CM. Patients with genetic findings should be aware of the potential for developmental delay. <i>ASPM</i> gene defect was the most common genetic cause of CM in this study. The estimation of the incidence of <i>ASPM</i>-CM in East China might provide a reference for analyzing overall incidence.