Over the last decade, significant advancements in Genome-wide Association Studies (GWAS) have been made, albeit with considerable diversity in cohort composition, genotyping strategy, and sample size. A primary challenge is the underrepresentation of non-European populations and limited availability of pregnancy and newborn phenotypic studies. Non-Invasive Prenatal Testing (NIPT) for fetal trisomies, utilizing maternal plasma cell-free DNA sequencing, has emerged as a globally adopted molecular test with over 10 million participants. Our previous research demonstrated the potential of low-pass Whole-Genome Sequencing data derived from NIPT for human genetic studies, identifying novel signals for traits such as height, weight, fertility, and maternal age. In this study, we broadened this approach to encompass a range of maternal and neonatal phenotypes and common pregnancy complications. We conducted a genetic analysis of 104 maternal and neonatal phenotypes from over 100,000 Chinese women, marking this as the largest such genetic study in the Asian population. Our GWAS revealed 407 genome-wide trait-locus associations, with 75.18% previously cataloged in the GWAS Database. An independent replication study validated 70 out of the 88 (79.5%) novel hits. Additionally, we investigated the genetic background of pregnancy complications, including Gestational Diabetes Mellitus (GDM) and Intrahepatic Cholestasis of Pregnancy (ICP). For GDM, our GWAS identified two candidate genes, and an ancient DNA analysis unveiled a mutation initially present in an ancient Chinese individual during the Holocene period, potentially providing insight into the genetic diversity of GDM across populations. For ICP, we replicated a known signal in the ABCG8 gene and discovered a novel association in SLC39A9. To facilitate further research, we've established a website for visualizing, sharing, and downloading the GWAS summary statistics. In conclusion, our findings underscore the power of leveraging NIPT data to gain genetic insights into maternal and neonatal phenotypes, accelerating future mechanistic studies into complex pregnancy traits and diseases.