Rare diseases occupy a critical position in global public health concern, profoundly influencing pediatric demographics, particularly in neonates. The rapid development of next-generation sequencing technologies in recent years has significantly enhanced the capacity for early detection and targeted treatment strategies for rare diseases. Globally, neonatal genome projects are being implemented with the primary goal of demonstrating the efficacy and benefits of gene sequencing technology in diagnosing genetic rare diseases. Specifically in China, the Genetic Counseling Branch of the Chinese Genetics Society, in partnership with the Children′s Hospital of Fudan University, launched the China Neonatal Genomes Project(CNGP). This project, including 100 000 cases and integrating extensive genomic data with detailed phenotypic information, aims to facilitate a thorough investigation of genotype-phenotype correlations in rare neonatal diseases. These initiatives will not only open new pathways for the early identification of genetic factors in rare diseases but also are instrumental in the advancement of precision medicine. Moreover, they may also contribute to the fields of pharmacogenomics and the understanding of adult-onset diseases. Based on various genotype-phenotype cohort studies undertaken by the CNGP, we review the data collection process related to genotype-phenotype in neonatal rare diseases and outline the advancements in previous cohort studies. We also intend to assess the present challenges on neonatal rare diseases, and propose insightful recommendations for future studies.