This study investigates the cellular heterogeneity and developmental trajectories of syncytiotrophoblast (STB) nuclei during human pregnancy using single-nucleus RNA sequencing (snRNA-seq) and single-nucleus ATAC sequencing (snATAC-seq). The research focuses on early and late pregnancy stages, revealing dynamic changes in STB nuclear subtypes and their corresponding transcriptional and epigenetic states. Key findings include the identification of master transcription factors (TFs) such as MITF, STAT5A, CEBPB, and FOSL2 that regulate diverse STB nuclear lineages. The study also confirms the presence of STB nuclear subtypes in human trophoblast stem cell (hTSC)-derived STB and trophoblast organoid-derived STB, highlighting the conservation of regulatory mechanisms. The results provide valuable insights into the heterogeneity of human STB and offer a resource for understanding pregnancy complications.This study investigates the cellular heterogeneity and developmental trajectories of syncytiotrophoblast (STB) nuclei during human pregnancy using single-nucleus RNA sequencing (snRNA-seq) and single-nucleus ATAC sequencing (snATAC-seq). The research focuses on early and late pregnancy stages, revealing dynamic changes in STB nuclear subtypes and their corresponding transcriptional and epigenetic states. Key findings include the identification of master transcription factors (TFs) such as MITF, STAT5A, CEBPB, and FOSL2 that regulate diverse STB nuclear lineages. The study also confirms the presence of STB nuclear subtypes in human trophoblast stem cell (hTSC)-derived STB and trophoblast organoid-derived STB, highlighting the conservation of regulatory mechanisms. The results provide valuable insights into the heterogeneity of human STB and offer a resource for understanding pregnancy complications.