Maternal nutrient restriction (MNR) heightens disease susceptibility in offspring through epigenetic modifications that alter the development of essential organs. This study investigates how restriction alters the fetal sheep hepatic methylome and its potential regulatory influence on gene expression. Using a monozygotic twin model generated through embryo splitting, we examined hepatic DNA methylation responses to maternal nutrient restriction (50% vs. 100% NRC nutritional requirements; n = 4 per group) from gestational day (GD) 35 to 135 in pregnant sheep. At GD 135, conceptus (fetal–placental unit) development was assessed; although fetal weight was unaffected (p > 0.10), restricted fetuses exhibited reduced liver mass (p < 0.05). Whole-genome bisulfite sequencing (WGBS) of fetal liver identified 1,636,305 differentially methylated CpG sites (dmCpGs) in the Group-Level Analyses and 42,231 dmCpGs in the Twin-Pair Analyses. At the Group-Level, 40,533 promoter, 126,667 exonic, and 785,381 intronic sites were identified, whereas the Twin-Pair subset contained 1314, 7116, and 22,239, respectively. Site-level shifts and functional enrichment across features highlighted GPCR–cAMP/calcium–PI3K/AKT signaling, phosphoinositide metabolism, ECM/integrin–focal adhesion networks, thyroid hormone signaling, and Rho-family GTPases. These findings indicate that maternal nutrient restriction modifies the fetal hepatic methylome through coordinated signaling, metabolic, and structural reconfigurations that create conditions conducive to metabolic disease.