EPA and DHA are long-chain fatty acids with health benefits on offspring underpinning the accumulative recommendations for their prenatal ingestion. Recent in vivo studies have emerged indicating a positive correlation of EPA and DHA with fetal BAT development, while other in vitro trials demonstrated their negative implication in promoting fetal myoblast reprogramming into adipoblasts. Therefore, the objective of this study was to test the effect of maternal EPA and DHA on fetal muscle development and energy balance. Two groups of Female C57BL/6 mice were assigned to different diets throughout the entire period of gestation and lactation; the first group was fed EPA and DHA enriched diet (FA); whereas, the other was fed a diet devoid of n-3 PUFA (CON). Embryos at day 13 of gestation and offspring at age of 1 and 21day were selected for sample collection and processing. No change in little number and body weight were observed between groups in newborns at day1, but a tendency to weigh loss in the FA group was detected after weaning. Transient increase in the expression levels of MYOD1, MYOG, MRF4, and MHC4 were observed at day 1 post-parturition (P<0.05). Except of IGF-1 P<0.05, the expression levels of genes regulating muscle protein synthesis and catabolism were comparable (P>0.05) between groups at day 1 and 21. Persistent increase in ISR expression (P<0.05) but not in GLUT-4 (P>0.05) were detected in day 1 and 21 age offspring. An increase in the expression of PPARγ and AP2 but not C/EBPα (P<0.05) at day 1 were observed. The three key regulators of basal adipogenesis were up-regulated in weaned mice (P<0.05). Up-regulation of PPARγ, AP2, and C/EBPα levels were accompanied by increasing intramuscular fat accumulation in day 1 and 21 samples. Considerable increase in the transcripts of genes regulating lipid catabolism and thermogenesis in liver including Cpt1α,Ehhadh, Mcad, Lcad, Acadvl, slc22a5, slc25a20, and Pparα (P<0.05) was noticed in (FA) group after 21 day of treatment; whereas, only the transcripts of Cpt1α andEhhadh increased in day1 neonates’ livers . Similarly, genes regulating lipolysis (ATGL and HSL, MGL and LPL) were up-regulated at day 21 of treatment only in (FO) group (P<0.05) while EPA and DHA maternal intake does not affect the expression of lipogenesis regulating genes (Fasn and Srebp1c) (P>0.05) in day 1 and 21 offspring. EPA and DHA treatment promoted BAT development and activity through increasing the expression of BAT signature genes including (UCP1, Cidea, Prdm16, Pgc1α, Dio2, Zic1, Fgf21, P2rx5, and PPARα(P<0.05). Also, maternal intake of EPA/ DHA enriched diet enhanced browning of sWAT by stimulating the expression of beige markers such as UCP1, Shox2, Tmem26, and PAT2 and thermogenesis regulating genes (PPARα, PGC1α, Cox7α1, and Cox8β) (P<0.05). Taken together, maternal ingestion of EPA and DHA may be suggested as a therapeutic option to encounter many pathophysiological disorders, mainly childhood obesity, and confer long-lasting metabolic benefits on offspring.