Schizochytrium sp. L. oil (SO), fish oil (FO), and sacha inchi oil (SIO) can regulate high‐fat diet‐induced obesity, but the effect on gut microbiota and the mechanism remain unclear. This study aimed to find out the different effects of the three oils mediated the gut microbiota on lipid metabolism. In comparison with the high‐fat diet (HFD) group, SO, FO, and SIO could reduce fat mass accumulation and decrease the levels of the serum and liver biochemical parameters in mice. The regulatory effect on gut microbiota in mice is determined by 16S rRNA gene high‐throughput sequencing. Caulobacter, Acetatifactor, and Mucispirillum as dominant bacterial genus are enriched in intervention groups. SO, SIO, and FO could distinctly decrease interleukin 6, nuclear factor‐kappa B, tumor necrosis factor‐alpha, sterol regulatory element‐binding protein 1c, FAS, and HMGCR expressions in liver, upregulate the expression of acyl‐coenzyme A oxidase 1 and A acetyltransferases and regulate the thermogenesis. SO, SIO, and FO has a comprehensive impact on lipid metabolism by the expression of genes related to fat synthesis, cholesterol synthesis, inflammation, energy consumption, the structure of intestinal flora, abundance of beneficial bacteria, and intestinal diversity. Based on these results, SO, SIO, and FO may be used as functional food to drive beneficial changes in gut microbiota and then regulate the lipid metabolism disorders.Practical Applications: Obesity‐related diseases caused by lipid metabolism disorders have driven the rapid development of the diet drug market. However, the side effects of diet drugs on the human body also make the majority of consumers worried. Natural oil products that regulate lipid metabolism disorders and dietary obesity provide a substitute. Schizochytrium sp. L. oil (SO), fish oil (FO), and sacha inchi oil (SIO) are rich in high‐quality unsaturated fatty acids and are not suitable for high temperature cooking but can be eaten in low temperature cooking and sauces and so on. SO, FO, and SIO can be used to develop functional food that could reduce lipid metabolism disorders.