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The objective of this study is to determine the effects of the dietary replacement of soybean oil (SO) with rubber seed oil (RSO) on the growth performance, carcass trait, and lipid metabolism in Pekin ducks. A total of 160 1-day-old Pekin ducks were randomly allocated to four experimental treatments and fed diets with different ratios of SO to RSO as follows: 3:0 (control), 2:1, 1:2, and 0:3. Dietary RSO supplementation had no effect on their growth performance; however, it significantly decreased the yield of abdominal fat (<i>p</i> < 0.05). As the dietary RSO increased, the plasma TG, CHO, LDL-C, and HDL-C contents of ducks decreased (<i>p</i> < 0.05). Additionally, the contents of total fat, triglycerides, and cholesterol in the liver and breast reduced in the ducks fed RSO diets (<i>p</i> < 0.05). Liver n-3 PUFA levels linearly increased (<i>p</i> < 0.05), while the n-6/n-3 PUFA ratios reduced with increasing RSO levels (<i>p</i> < 0.05). Moreover, dietary RSO supplementation resulted in decreased gene expressions of <i>FABP1</i>, <i>ME1</i>, <i>SREBP1c</i>, <i>FASN</i>, <i>DGAT2</i>, and <i>HMGCR</i> (<i>p</i> < 0.05), while there was an increased expression of the <i>ABCA1</i> gene (<i>p</i> < 0.05) in the liver of the ducks. In conclusion, dietary RSO supplementation reduced fat deposition and enhanced n-3 PUFA levels without affecting the growth performance of Pekin ducks.