BACKGROUND: Increased backfat thickness of sows in early gestation is negative to reproductive performance. Endometrial receptivity is an important determinant of reproductive success, but it is unclear whether the effect of sow backfat thickness on litter size is associated with endometrial receptivity and whether melatonin treatment may have benefits. The present study seeks to answer these questions through in vitro and in vivo investigations. RESULTS: Excessive lipid deposition and lower melatonin levels in the uterus are detrimental to endometrial receptivity and embryo implantation in high backfat thickness sows. In cells treated with melatonin, the MT2/PI3K/LIF axis played a role in reducing lipid accumulation in porcine endometrial epithelium cells and improved endometrial receptivity. Furthermore, we found a reduction of lipids in the uterus after eight weeks of intraperitoneal administration of melatonin to HFD mice. Notably, melatonin treatment caused a significant reduction in the deposition of endometrial collagen, an increase in the number of glands, and repair of the pinopode structure, ultimately improving endometrial receptivity, promoting embryo implantation, and increasing the number of litter size of mice. CONCLUSIONS: Collectively, the finding reveals the harmful effects of high backfat thickness sows on embryo implantation and highlight the role of melatonin and the MT2/PI3K/LIF axis in improving endometrial receptivity by enhancing metabolism and reducing the levels of uterine lipids in obese animals.