In this study, the effect of sn-2 palmitic triacylglycerols (sn-2 palmitic TAGs) and the ratio between the two major sn-2 palmitic TAGs (OPL to OPO ratio) in a human milk fat substitute (HMFS) on growth, fatty acid and calcium absorptions, and lipid and bile acid metabolic alterations was investigated in Sprague-Dawley rats. After 4 weeks of high-fat feeding, rats fed with the HMFS containing a sn-2 palmitic acid content of 57.87% and an OPL to OPO ratio of 1.4 showed the lowest TAG accumulation in their livers and hypertrophy of perirenal adipocytes, compared to the groups fed with fats containing a lower sn-2 palmitic acid content or a lower OPL to OPO ratio. Meanwhile, synergistically improved absorption of fatty acids and calcium and increased levels of total bile acids (BAs), especially for the tauro-conjugated BAs (TCDCA, TUDCA, TαMCA, TβMCA, TDCA and TωMCA), were observed in rats by both increasing the sn-2 palmitic acid content and the OPL to OPO ratio in HMFS. In addition, the levels of total BAs and tauro-conjugated BAs were negatively correlated with serum TAG, TC, and LDL-c levels and positively correlated with HDL-c levels according to Spearman's correlation analysis (P < 0.05). Collectively, these findings present new nutritional evidence for the potential effects of the TAG structure and composition of a human milk fat substitute on the growth and lipid and bile acid metabolism of the host in infancy.