Conjoined twins represent an exceedingly rare subtype among monozygotic twins. Current research on conjoined twins predominantly focuses on prenatal imaging diagnostics and postnatal surgical separation. Given that conjoined twins arise from the same fertilized egg, their genetic material is nearly identical. Few people pay attention to the differences in conjoined babies. Moreover, there is limited research into the molecular characteristics of conjoined twins. Recently, research focused on a comprehensive series of molecular genetic tests on a pair of conjoined twins that was terminated at 15 weeks and 4 days of gestation. Each specimen underwent multiple rounds of genomic sequencing to investigate the associations between DNA methylation, transcriptomics, and exon region mutations in the conjoined twins. All studies were conducted with ethical approval and adhered to relevant ethical guidelines. The results showed similar global methylation patterns in the two conjoined fetuses, but significant differences in specific local regions, such as CpG islands (P = 0.026), enhancers (P < 0.001), and various repetitive elements (P < 0.05). The conjoined twins exhibited significant disparities in terms of DNA methylation and gene expression levels in areas related to growth, development, cellular morphology, and cellular stress responses. Whole-genome exon sequencing revealed that common mutations in the conjoined twins primarily occurred in processes associated with neural development, lipid metabolism, and microtubule formation. Specific mutations were correlated with the biosynthesis of cellular components, behavior, and germ cell development. This study provides the first insights into the molecular characteristics of conjoined twins, elucidating the epigenomic similarities and differences between the two fetuses. These findings offer valuable resources for future researchers investigating the pathogenic mechanisms of conjoined twinning.